Revealing mistake: Near the start, when Trinity runs away from Agent Smith, jumps off the building, crashes through the window, rolls down the stairs and gets out two guns, when she jumps from the building, it is obviously a stunt double.
Continuity mistake: When the guard asks Neo to remove any metallic items after he sets off the metal detector, Neo's coat is open, and he's just got a T-shirt on, with no guns strapped to him. In the closeup, all the guns are visible. Most are down the side, but we should have seen the pistols in his belt from the earlier angle. If nothing else, with his coat open as much as it was, the guard should have spotted the weapons even before he opened it further...
Continuity mistake: When Cipher is making the deal, one second he is holding his cigar in his right hand, then all of a sudden it is in his left.
Visible crew/equipment: When Neo and Morpheus are in the training program with the girl in the red dress, after Morpheus has paused the program you can see a camera and a black fabric cover around it reflected off Morpheus' sunglasses for a considerable amount of time. Noticeably in the shot considerably close to his face while talking.
Visible crew/equipment: When Trinity and the other guys are taking the bug out from Neo's stomach, as it is coming out, if you put it in slow-motion, you can see (it's not really clear, but you can see a light reflecting off it) a string pulling the bug up.
Visible crew/equipment: When Trinity asks Neo 'How did you do that?' after he's dodged the bullets the white reflective screen is visible in the left lens of her glasses.
Continuity mistake: After Neo and Trinity kill all the agents with the helicopter when they rescue Morpheus, you see Morpheus breaking the chain of his handcuffs. He still has the cuffs on his wrists. But then in the next shot of him, the handcuffs are gone.
Continuity mistake: When Neo and Morpheus are in the matrix simulation program, look at the people behind Smith as he draws his weapon. Normal. Then, when he is frozen and Neo looks back at him, you will see that all of the people are facing towards Neo or walking towards him.
Other mistake: In the bullet-time sequence in the subway station the lighting on Neo and Agent Smith doesn't change even as they spin round each other, principally because they were in a green screen chamber with even lighting to shoot the movie. It sticks out because the lighting on the CGI set (for the bullet-time shot) is pretty dim with light in specific areas.
Continuity mistake: When Agent Smith has Neo in a headlock on the train tracks in the station there is blood coming out of Neo's mouth and going down his chin. In the next shot the blood is almost completely gone apart for a little bit on his lips and a spot of it on his chin.
Continuity mistake: When Trinity runs sideways up the wall in the lobby under massive gun fire, the marble tiles on the wall move.
Continuity mistake: In the Oracle's house there is something wrong with the glasses in the cupboard behind Neo. When he's looking at the children, there are three small glasses in front, a big one behind and something else beside them. In a shot from below when the boy hands the spoon to Neo, the big glass has now moved to the left of the small ones.
Continuity mistake: When Smith put his glasses on the table while he is talking with Neo, the glasses are near Smith. When Smith takes them back, they are further away.
Visible crew/equipment: When Neo first holds the little boy's spoon the white screen is visible in the reflection.
Continuity mistake: When Neo tells tank that they need "Guns, lots of guns" he cocks the MP5 that he picks from the rack. It is matte black, but when the camera focuses in, it is shiny and reflective.
Continuity mistake: When Trinity is speaking to Neo near the end of the film when he is "dead", her hair falls from behind her ears then goes back again then is slightly off again.
Continuity mistake: When Trinity leaves the matrix at the start through the phone booth, the garbage truck driven by the agents rams the phone booth and punches a big hole in the brick wall. When the truck reverses there is no visible damage to the truck, not even a broken headlight, even though it has just crushed a phone booth and a brick wall.
Audio problem: In the club scene where Trinity introduces herself to Neo, she leans in to whisper into Neo's ear. Trinity's jaw in the shots from behind her is moving nowhere close to how it should for the words she is saying.
Continuity mistake: In the beginning of the movie, where Trinity runs from the agents, she jumps towards a window. She turns slowly in the air, eventually facing upwards when she crashes through the window, no longer turning. From the inside shot, however, she comes through it face down (so she can roll forwards down the stairs).
Continuity mistake: When Neo is about to be interrogated, Agent Smith throws Neo's file onto the table. In this shot, the piece of cord holding the file together points upwards, moments later it faces to the side.
Continuity mistake: When Neo falls during the jump program, after he finally lands on the concrete his left arm sleeve is pulled down midway. The camera then does a close-up of Neo, and his shirt has fixed itself and is now to his wrist.
Continuity mistake: Near the end when Neo runs and jumps into Agent Smith's body, the other two agents are shown standing at the end of the hallway. If you look closely at the shot of the agents after Agent Smith explodes, the tie clip of the agent on the left side of the screen is angled diagonally across his tie. Neo flexes the walls, and in the next shot of the agents the tie clip has returned to where it should be - horizontally across the tie.
Continuity mistake: As Neo awakens inside his "goo tube", a few from overheard shows him raising his arms against the covering of his tank. The shot changes to one from the front and suddenly Neo is in a sitting position and raising his arms up as he breaks the covering. When Neo was first raising his arms, he was laying on his back.
Continuity mistake: When Trinity is making a getaway from the agents, she is not carrying a weapon, neither is there a sign of one. But after she jumps over to the next building, she magically pulls two big handguns out of her leather suit.
Continuity mistake: In the very begining when the green computer writing comes up while trinity is making her call it says it's about 13:00 hours, but when she's running on the rooftops 5 minutes later, it's more like 1:00 am.
Visible crew/equipment: When Neo is at the office, while in his cubicle, he gets an express delivery. As he signs for it you can see another arm laying on the desk behind him. In the next shot he hands back the clipboard, you see it is only him and the delivery man. [Only visible in 4:3 format.]
Continuity mistake: When Neo first enters the construct, Morpehus and Tank plug him in. In the construct, Neo turns around a second after being plugged in, and Morpheus is now standing there. There's no way he could have loaded up that fast.
Continuity mistake: 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 closeup of the keys show keys from a standard keyboard that are clearly not the keys on a Natural Keyboard Pro.