Continuity mistake: When Agent Smith is interrogating Neo, after Smith has sealed Neo's mouth shut and he is backed into the corner, when the camera cuts back to Smith you can clearly see a reflection in his glasses of Neo still sitting down in the chair.
Visible crew/equipment: When Neo is going to open the door to enter the Oracle's house, you can clearly see a camera on the doorknob. There's a sheet over it painted to look like the wall behind it, with a representation of Morpheus' tie too, because he's blocked by the camera.
Continuity mistake: When Neo is out on the scaffolding and loses his phone, the first shot down is of an empty street, in the shot of the phone falling the street is filled with people and a big parade, then it cuts to a wider shot and the people have vanished again.
Revealing mistake: During the rooftop rescue, when Morpheus is hanging from Neo's arm (who is hanging from the helicopter), a safety wire is visible running out of Morpheus' sleeve and into Neo's hand.
Continuity mistake: When Morpheus is fighting the agent in the bathroom of the building they were trapped in, the agent punches through a brick wall, yet next time we see the wall, there is no damage.
Visible crew/equipment: When the 3 agents visit the roof top where Neo saved Trinity from the chopper, you can clearly see the camera crew in the agents' sunglasses.
Continuity mistake: When Neo comes to work he glances at the name of his company. The sign says Metacortex. When Neo is running from the agents there is a sign on the back wall which says Meta Cortechs.
Revealing mistake: During the fight scene between Neo and the agent in the subway station, after Neo incapacitates the agent and flips out of the way of the oncoming train, you can see where the wire harness connected to his back. You can also see one of the wires visible by his wrist.
Continuity mistake: The first time Neo comes out of the Loading Program, and is about to throw up, it shows you a shot from his eyes and the floor is clear of anything, and then it does a shot of him throwing up and he does so on a bunch of wires. The angle changes too - the POV shows all the lines in the grate at about 45 degrees, but when he throws up, they're all horizontal in relation to him.
Other mistake: Whenever Trinity confronts the agent on the rooftop and says, "Dodge this", she points her gun to temple of the agent while his head is turned to her. He glances back, but never fully turns his head. The next scene shows him being shot facing Trinity...with a shot in middle of his forehead. Some people think it's to do with the angle he enters the soldier's body to start with, but the angle change is visible before he changes back into the original body.
Continuity mistake: When Neo is fighting the agent in the subway, he wipes his blood on the back of his hand, but when he puts his fists up the blood is gone.
Continuity mistake: Shadows move about during the rooftop battle - easiest benchmarks are the shadow stretching towards us from the chimney-type thing at the start, then Trinity's stretching horizontally after she throws the knife at the remaining trooper.
Other mistake: When Neo comes back from the conversation with the oracle, a part of the cookie, which he has got from the oracle, is bitten off. A few seconds later he wants to eat the cookie and there is no sign of a bite anymore.
Continuity mistake: When Tank comes in to talk to Neo about training in Neo's cell, the strap on Tank's shoulder moves from being on his skin when he's in the doorway to on his shirt in subsequent shots.
Continuity mistake: When Mouse is in the room with the brick window, he drops one long box that is assumed to be full of guns. The scene cuts to Tank and then Mouse again. When he gets out the guns, he pushes 2 smaller boxes off the long box which weren't there before.
Other mistake: When Neo is running along while shooting, it switches to a shot of a soldier firing a shotgun. Just before Trinity kicks it out of his hands, he's firing at the same spot over and over. Trinity is behind him, and Neo is moving, so what is he shooting at?
Plot hole: When Morpheus and his crew rescued Neo from the Matrix, how was it possible that Neo's real self had his ear pierced?
Revealing mistake: When it is Neo's turn to make the Jump he takes a run up, and the camera changes to a brief sideshot of him running across the top of the building with the sky behind him. There is a big fuzzy blobby outline around him which should have been edited out.
Continuity mistake: In the beginning of the movie when Neo gets the FedEx envelope, he is shown at his desk opening the envelope and then pouring it out. As he is pouring the phone out, with the green packing label on the top, the shot cuts "seamlessly" to a close up of the phone being poured out the rest of the way. However, the envelope is now flipped over. The FedEx logo is now on top (the packing label is facing down).
Continuity mistake: In the kitchen scene with Neo and the Oracle, the Oracle is baking cookies. When the Oracle takes the cookies out of the oven and brings them to the table there are 4 cookies on the plate. As she offers a cookie to Neo there are 6 cookies on the plate.
Continuity mistake: In the interrogation room. Mr. Smith has a green file with him with Neo data accumulated. Smith opens the file and leafs through a few sheets, without removing any, but in subsequent shots we can see that some sheets have been removed from the file and put on the left.
Continuity mistake: When Neo is brought out of the building, you clearly see the police officer push the car door open and turn his head to the rear of the car, yet in the next cut where we are viewing the scene from the reflection in Trinity's side view mirror his head is facing forward again.
Factual error: When Trinity is being arrested, you hear the cops all burst into the room and cock the hammers on their Glocks. The Glock doesn't have an external hammer. To load the weapon, you have to pull the slide back and release it.
Continuity mistake: On the skyscraper, when Neo and Trinity kill all of the soldiers, Agent Brown comes to the roof. Neo immediately draws his guns and fires until both of his clips are empty. After that, Neo drops his guns, just as Agent Brown aims at him. During Bullet-Time there are no guns on the floor. When he hits the ground, then the guns are left and right of his legs.
Continuity mistake: When they are down on the ground shots they show everyone driving on the right side of the road, but when there are aerial shots, you can see everyone driving on the left side of the road.
Continuity mistake: When Morpheus first takes Neo into the Construct and is explaining it all to him, you can see Neo's reflection in his glasses, but when the camera shows Neo, he is wearing different clothes and standing in a different position and moving.
Audio problem: In the lobby shootout scene, when Trinity starts kicking one of the guards after he goes to reload and reaches for a new clip, you can hear her yell the first time she kicks him, but the next two times, although her mouth opens the same way, the audio's been silenced.
Continuity mistake: As Neo fights the guards in the main floor of the government building, he does a one handed somersault while shooting at the guards. If you watch closely on a shot behind Neo, he is aiming his gun way off to the right side yet still manages to shoot the guards.
Continuity mistake: When Neo is on the ledge outside of the office trying to follow Morpheus's instructions, he wraps his hand around the pillar to attempt at making a pass. If you look, you can see multiple hand prints from where Reeves had repeated the shot over and over.