- Continuity: In the first scene in which Neo appears, we see him from above, sleeping in front of his computer. The keyboard he is using is a Microsoft Natural Keyboard Pro with the atypical curved key configuration. When messages begin appearing on his screen, he tries to stop them by hitting various keys, but the close-up of the keys show keys from a standard keyboard that are clearly not the keys on a Natural Keyboard Pro.
- Continuity: When Neo (Anderson) is first handed the FedEx envelope, he moves his hand to the corner to open it - then the camera shifts, and he moves his hand to the corner to open it.
- Continuity: When Neo first meets Morpheus, they shake hands. We see Morpheus from behind, and his left arm is behind his back. Then we see Morpheus from the front, and his left arm is straight down at his side. Then we see Morpheus from the back again, and his arm is once again behind his back.
- Crew or equipment visible: When Neo is examining the spoon prior to bending it, a crew member dressed in black - probably the cameraman - is reflected in the spoon.
- Continuity: When Neo is being shot and is subsequently "killed" there is a shot showing the cartridges leaving the Smith's pistol. One of the cartridges is clearly a spent blank with crimping rather than a spent live bullet cartridge.
- Crew or equipment visible: When Neo backflips off the train tracks onto the platform, at the end of the flip, a few inches of the wires can be seen either side of his hands.
- Continuity: After Trinity crashes through the window, tumbles down the stairs and then points her guns back toward the window, we cut to a close shot of the top of the stairs showing a hanging light fixture swinging back and forth. A few seconds later, during an over-the-shoulder shot from Trinity's perspective, the fixture is perfectly still. The sound and image imply that it did not start swinging until she reached the bottom of the stairs.
- Continuity: In the scene where Neo has hundreds of acupuncture needles in his body, needles disappear from his head. The comments on DVD indicate that all of the needles were a prosthetic device except for the ones in his head. The real needles are there when the camera looks at him from the side, but then disappear as the camera moves in.
- Revealing mistakes: During the Agent/Trinity chase, when the last police officer fails to completely jump across, his legs cause the "brick" wall to vibrate noticeably.
- Boom mike visible: While showing Neo what has happened to his real world, Morpheus looks to the sky and remarks: "Fate, it seems, is not without a sense of irony." As he looks up, you can see the boom mike reflecting in his sunglasses.
- Continuity: When Morpheus attacks Smith to save Neo, Morpheus headbutts Smith and knocks his glasses off (camera angle behind Morpheus). But then there is a shot from Smith's POV and his glasses are on again, then the camera shifts to Morpheus' view and they're gone again.
- Revealing mistakes: During the beginning scene, when the officers are chasing Trinity on the rooftops, over their heads, you can see that the sky is really the ceiling of the soundstage painted black.
- Incorrectly regarded as goofs: After Morpheus is rescued from the Agents, the blood and marks on his face are gone. He's been under a huge stream of water that probably washed them away.
- Continuity: Near the end of the subway fight scene, Agent Smith throws Neo into a wall after which he falls onto the rails along with debris from the wall, but when Neo backflips onto the platform, the debris is neatly positioned by the wall.
- Continuity: During the lobby shootout, Neo cartwheels while firing an M-16 rifle at some guards, however, one shot shows Neo firing in completely the wrong direction.
- Continuity: During the lobby shootout, Trinity sneaks up on a soldier who is reloading and kicks his M-16 rifle out of his hands. In some shots, the guard is still holding the gun, but in other shots, he isn't. However, when Trinity knocks him out and he hits the floor, the M-16 clearly is still in his hands.
- Errors in geography: The Matrix is apparently simulating some unknown American city (the accents of the characters, references to one phone call, IRS, and Social Security number). However, the sign near the elevator button refers to a "lift," a rooftop sign says "authorised," an ATM has a sign for an Australian bank, and cars are seen driving on the left (or, when Neo drops the phone, on the right against the road markings). When the policeman yells "Freeze!" in the opening scene with Trinity, the actor's Australian or New Zealand accent is obvious, and when the guard in the lobby calls for backup, the accent is again very obvious. Finally, in the last scene, where Neo makes the phone call, after he hangs up there is a clear shot of the Sydney Harbour Bridge in the background. Arguments for these inconsistencies being part of the Matrix and hence not problems don't wash, since the Matrix is trying to be accurate (else why make it so much like the "real" world).
- Continuity: When Agent Smith is interrogating Morpheus, he has his hands on his head, his index finger is in front of his ear in the shot from behind, but in the shot from the other direction, his index finger is behind his ear.
- Crew or equipment visible: When Neo reaches to open the door to the Oracle's apartment, the lens of a camera is visible. The camera itself seems to be covered with green cloth to match the color in the hallway, and even has a yellow tie painted on it to match the one Morpheus is wearing, since he is standing behind the camera.
- Continuity: When Neo is being interrogated by the agents, Agent Smith plops a folder on the table. When he opens it, there are no pages on the back of the cover. When the camera shifts as Agent Smith is looking through the pages, we see several pages on the back of the cover that Agent Smith never placed there.
- Continuity: In the lobby battle, when Neo fires the two small machine guns with long barrels and curved magazines, the shell casings are far too long; these weapons are Czech Skorpions in 7.65mm (.32 caliber). In addition to being too long, the neck of the shell bottlenecks (slopes downward) about 2/3 of the way down, while 7.65mm shells have no bottleneck. These shells could very well come from the M-16 Neo fires later.
- Factual errors: When Neo is fighting the agent in the subway scene, they shoot at each other in bullet time. Though there are bullets coming out of the pistols, the actions of the pistols (the top part of the gun that slides back to allow the spent cartridge to spring out of the barrel) are not moving to let the pistol reload. In addition, there is no recoil.
- Revealing mistakes: Less than a second before Neo jumps off the building in "the first jump," special effect artifacts are briefly visible around him. (As he's running, side view, against the sky.)
- Continuity: When Morpheus and Neo are in the Agent Training program, the first shot of Neo you don't see a dove in the reflective glass behind him, in the second shot you see one.
- Incorrectly regarded as goofs: Cypher couldn't use the chairs by himself to go inside the Matrix. We see Cypher typing on the keyboards, watching the Matrix in code. He tells Neo that you have to look at it in code when you are not inside, therefore justifying that he might be interacting with the Matrix through the keyboard; he is not obligated to enter the Matrix in order to change events. Trinity talks about "shifts" at the beginning of the movie, also suggesting that she can go inside the Matrix without the aid of Tank. Cypher presumably gets an inferior sense of taste and smell compared to what he would have if he were actually plugged in, or he'd have no reason to deal.
- Continuity: When Neo drops the phone, the first time you see the phone falling, there is a parade marching in the street below. Cut immediately back to Neo, the street is empty.
- Continuity: Numerous differences between sunglass reflections and the surroundings.
- Crew or equipment visible: As Neo passes the camera while falling during the "Jump Program," his shirt is blown open by the wind and clearly shows the harness he is wearing underneath.
- Incorrectly regarded as goofs: When Neo is rescuing Trinity from the falling helicopter, he slides across the roof of a building. When he reaches the edge, his foot hits the block causing it to move, but in a way consistent with a real block whose grout is imperfect; after all, that's a rather large force.
- Continuity: After Neo is shot by Agent Smith, Trinity leans close to whisper. Her hair begins to fall over her face. Cut to another angle and her hair is back in place again.
- Continuity: Just before the door to the Oracle's apartment opens, Morpheus has his glasses on. After the door opens and the camera angle switches, his glasses are in his left hand (visible after Neo crosses in front). Presumably he snatched them off in the same move that instantly took his arms from a 90-degree angle to straight down.
- Continuity: Cypher's cigar changes hands in the restaurant.
- Continuity: The piece of meat Cypher eats at the restaurant changes from one shot to the next.
- Revealing mistakes: When Neo is running from the agents, he jumps off a fire escape, and when the camera flashes further away you can clearly see the thick gray mat used for the fall.
- Incorrectly regarded as goofs: The Massive Attack song "Dissolved Girl" playing in Neo's headphones is track 6 on the album, not track 5, and the timing on the counter is off in relation to the actual song. Given Neo's equipment, it could well have been a homemade custom CD.
- Continuity: When his boss, Mr. Reinhart, is lecturing Thomas Anderson, Anderson's hands are in front when seen from outside and from the rear, and behind him when seen from Mr. Reinhart's desk.
- Continuity: When Morpheus and Neo move from the dojo to the jump program, the shot from their viewpoint looking down shows them landing far from any roof structures, on a building much higher than any nearby. The next shot of Neo shows them to be right next to a structure, on a building about as tall as one right across the street.
- Continuity: While Neo is on the way to the Oracle, his sideburns change length and shape.
- Continuity: When Morpheus is showing Neo the construct, there are no shadows (even under their feet). However, when Neo wants out, he steps back and there are shadows under his feet.
- Continuity: When Trinity learns how to fly the helicopter, she is given instructions to fly a B-212 (which is what's shown) with a Bell JetRanger image on the computer.
- Continuity: When Neo is leaving the Oracle's apartment, the cookie in his hand (down by his side) has a bite taken out of it. A few seconds later, Neo brings the cookie up to take a bite - and it is whole.
- Incorrectly regarded as goofs: The computer screen gives the time of Trinity's phone trace as 13:24:18. While it is dark outside, that time could be UTC.
- Continuity: As the team prepares to visit the Oracle, we see Tank "loading them up" pressing buttons on the various keyboards around him. Before the last cut, his right hand is up, pressing buttons while his left hand is down. When we cut to the shot above Tank, his left arm is up and his right arm is down.
- Continuity: The gun Neo is handed as the police attack is a Sig-Sauer, but in later shots he is using a Glock, and then a Sig again.
- Revealing mistakes: A security guard calls for help on his radio at the beginning of the lobby shootout. He is wearing knee pads underneath his uniform.
- Incorrectly regarded as goofs: The chain of ammunition for the gun in the helicopter does not feed directly into the gun; it goes through a feeding mechanism between the ammo box and the gun. Further, the shells that drop are indeed spent; they have a bottleneck shape that confuses some viewers.
- Revealing mistakes: During the fight scene in the subway, as the Agent is about to punch through the concrete post, the section to be punched out is clearly visible.
- Crew or equipment visible: When Neo is holding Morpheus outside the helicopter, a safety cable is visible as a black line along Morpheus's arm going up to Neo in the last long shot before Neo lets go.
- Continuity: In the "dodge this" scene, Trinity's gun changes from a Beretta 92F to a Beretta 84F.
- Continuity: When Neo backflips out of the train's way, the distance between him and the train changes.
- Continuity: When Agent Smith fires his gun at the helicopter, the bullets hit on Trinity's right side, but when Trinity reacts to the shots, she looks to her left.
- Continuity: After Neo steals a man's cellular phone and the agents shoot at him, we see him running down an alley with the back of his shirt untucked from his pants. As he kicks in the door, his shirt has tucked itself back into his pants.
- Incorrectly regarded as goofs: During the rescue of Morpheus, at one point Trinity is seen to use both hands in controlling the flight stick of the helicopter. While a helicopter normally requires use of two sticks to control, in the kind of emergency situation shown, the collective (controlling up/down motion) can be temporarily ignored.
- Continuity: Blood on Neo's mouth as the subway approaches.
- Factual errors: People seem to physically recover in this film from very severe traumas, that normally would disable them. We see Tank take it twice, and then he is completely healthy (he's even in the "real" world, with no visible signs of damage). Morpheus takes a slug in the leg in the helicopter jump, but recovers easily. Neo is grazed twice in "bullet time" but it doesn't hamper him at all. The injuries to Morpheus from the torture also don't show up in the real world.
- Continuity: The width of Cypher's beard.
- Continuity: When Neo is in the old Lincoln with Trinity, Switch, and Apoc, Trinity says, "Apoc, lights." A close-up of the light switch follows. The external lights should be off because the switch is all the way in, yet it is night and the lights have been shown to be on. Apoc then pulls the switch halfway out, which would turn on the exterior running lights only, not the interior lights. He should've turned the switch, not pulled it.
- Incorrectly regarded as goofs: On Neo's introduction to the Construct, Morpheus jacks him in, then shows up in the Construct himself almost immediately, far quicker than he could have jacked in himself. But it's quite possible Neo was held in some kind of limbo until Morpheus was ready to join him.
- Continuity: After Neo fights Agent Smith in the subway, he is about to run up the right side of the steps. He stops to look at the subway train, sees Agent Smith get off the train, then turns to run up the center of the steps without moving sideways.
- Continuity: When Neo is interrogated by the agents, the reflection in Agent Smith's glasses do not correspond to the action in the editing. For instance, we see Neo standing in one shot, but the reflection in Agent Smith's glasses shows Neo sitting in the next shot.
- Revealing mistakes: In the lobby scene, after Neo has jumped in the air to kick the last guard, the guard drops his gun and the nozzle bends when it hits the ground, showing the gun to be rubber.
- Continuity: When Neo is flushed from his cubicle and fished up with the claw from a hatch in the Nebuchadnezzar he is passed out. But as he enters the ship he clearly moves his feet to avoid hitting the rim of the hatch.
- Crew or equipment visible: The "reflection" of Neo's hand on the knob of the door to the Oracle's home shows a hooded camera operator.
- Continuity: When Morpheus escapes the military building he snaps his handcuffs but they remain on. When Neo grabs Morphous, in mid air, no handcuffs are visible. The handcuffs re-appear when Neo drops Morpheus onto one hand.
- Crew or equipment visible: When Morpheus and Neo enter the white construct room the camera crane is reflected in Morpheus' glasses in several shots.
- Continuity: At the end of the Oracle scene, Neo takes one of the cookies that have just come out of the Oracle's oven. Seconds later, he bites into it and it snaps as if it were cold. If it had indeed come out of the oven a few minutes earlier, it would still be soft.
- Continuity: When Neo opens fire from the helicopter, and the glass begins to break, none of the three agents is visible (though they should be) and the chair in which Morpheus should be sitting can be seen to be empty.
- Crew or equipment visible: Dolly track, camera, and crew reflected in Neo's sunglasses after putting them on at the end of the film, when he steps out of the phone booth.
- Continuity: When Trinity tells the Agent to "Dodge this", his back is to her when he turns his head; she places her gun to his temple. In the next shot, when Trinity shoots him in the middle of his forehead, he is plainly facing her but he is never shown to have turned around.
- Crew or equipment visible: When Neo sits at his desk and receives the envelope with the phone in it, a crew member's hand is leaning on the left corner of his desk. (VHS version)
- Continuity: When Neo is being bugged the progression of the bug is inconsistent between shots.
- Continuity: As Morpheus introduces Neo to the Construct, his glasses are completely dark. The following shot they suddenly turn highly reflective. This was because, for that shot, the glasses were painted black to avoid the cameraman from being reflected in them.
- Continuity: After Neo is brought into the real world, Tank comes to introduce himself; while they're talking, the strap on Tank's right shoulder repeatedly jumps from the middle of his shirt sleeve to the edge between shots.
- Factual errors: An error in language really, the Oracle at Delphi (in Greece) prophesied with the words 'Know Thyself' above the entrance to the Temple of Apollo situated there. But these words were in Greek, 'Gnothi se auton', not the Latin appearing on the sign in the movie. It is incongruous to change the language for the film as the classical reference to The Oracle is then obscured for no reason.
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