Continuity mistake: During the fight scene in the train station between Agent Smith and Neo, after a lot of fighting Neo is thrown back and throws up blood. He then gets up and wipes it off with the back of his hand. Straight after that, it isn't visible anymore. It's completely vanished. (01:56:30)
Continuity mistake: In the subway fight scene, the shot where the agent is holding Neo down while the train is coming, you can see the Agent's tie in front of his arms, in the shot just as Neo is getting ready to jump with the agent you can see the agent's tie neatly pinned back with a tie clip. (01:57:48)
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. (01:59:05)
Continuity mistake: In the scene following Neo's death and 'rebirth' he stops the bullets fired by the agents and they fall to the floor. However when we see Neo walking forward, the bullets have disappeared along with the blood stain on the wall from when he was shot. (02:00:45)
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. (02:01:20)
Continuity mistake: When Neo puts his glasses on at the end and looks up you can see a blonde woman walk behind him left to right. In the very next shot from above him there is no one behind him except a large empty pavement. The woman has disappeared. (02:03:45)
Continuity mistake: Ground level shots 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 rooftop when Neo and Trinity are trying to save Morpheus, one of the Agents starts shooting at Neo. You can see the glass behind Neo doesn't shatter whilst he is shooting.
Continuity mistake: When Morpheus shows Neo the agent training simulation, the girl in red turns into an agent. When they pause the simulation you can see the reflection of Neo with a gun pointed at his head in Morpheus' glasses. When you look in one shot there is a visible white line/mark (scenery?) between the gun and Neo, in the next shot it is gone and then right at the end in the final shot it's back again.
Continuity mistake: Near the start, when Agent Smith jumps over the building and the police officer in the front says, "It's impossible," look closely in the background when the agent lands. You can see it's a different officer than the one that said it.
Continuity mistake: When Neo and Morpheus are going to see the Oracle, they approach the elevator. Neo is standing on the right and Morpheus is standing on the left. Yet when they enter the elevator, Morpheus and Neo both come from the right.
Continuity mistake: In the beginning, Neo opens the FedEx envelope twice.
Continuity mistake: When Neo is in the helicopter firing the automatic weapon into the building he is moving the gun horizontally. The bullets strike vertically, though, starting from the floor near the window and traveling upwards towards the back wall of the room. There are two shots that show this.
Continuity mistake: In the scene right after Neo steals a man's cellular phone, we see him running down an alley with the back of his shirt untucked from his pants. After cutting back from the agent who's chasing him, we see that Neo's shirt has miraculously tucked itself back into his pants.
Continuity mistake: When Tank comes into Neo's room and talks to him, just before his training, note that there is a rip in Tank's shirt near his right shoulder. Near the end of the scene, the shot changes to Neo, then when it cuts back to Tank, there's no rip. When it cuts to Neo and back to Tank again, the rip is there.
Continuity mistake: Near the end of the movie after agent Smith shoots Neo. Trinity is whispering to Neo, as she leans toward him there is a small strand of hair on Trinity's right temple slowly falling down on her face. The shot changes to Neo's face and back to Trinity where her hair is now perfectly in place and the strand is gone.
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: The subway train that "kills" Agent Smith doesn't pull away from the platform. It simply disappears.
Continuity mistake: After Neo gets shot on the rooftop you see a wound on his right shoulder. However when he was fighting Smith in the subway station, it was gone (seen when he is standing up wiping blood from mouth). Then it comes back when he is running from the agents.
Continuity mistake: When Neo is following Morpheus' instruction to escape the agents who have come to arrest him at work, the location of the knot in his tie changes - note the pattern.
Chosen answer: The pills are the Matrix representations of computer programs. The red pill contains code designed to disrupt Neo's input/output signals, so that Morpheus' team can pinpoint his physical location in the real world. Once located, a signal of unspecified type is sent from their ship, which presumably serves to wake Neo up.
Tailkinker ★