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). (00:12:50)
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. (00:16:00)
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: 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. (01:41:50)
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. (00:16:50)
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. (00:42:25)
Continuity mistake: When 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 instant next shot shows him being shot facing Trinity with the gun in the middle of his forehead. (01:42:20)
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. (01:16:15)