Continuity mistake: At the beginning of the film when we see the motorbike come off from the top of the parking lot, in the overhead shot we see Trinity jump off and land after the two lamp-posts. In the following shot when she lands, she lands before the lamp-posts. (00:01:35)
Visible crew/equipment: In the scene near the beginning of the film where Morpheus is discussing the machines tunelling down to Zion with the other captains, you can see the camera in the reflection of his sunglasses in multiple shots. (00:06:50)
Continuity mistake: At the beginning, Agent Smith approaches the metal door. On the wall to one side is the writing "Muz 25", on the other side a wire ends in a light switch. After the fight, Neo kneels in preparation for flight and the light switch has vanished. (00:08:10 - 00:10:45)
Revealing mistake: After Neo has knocked out the first two agents after the meeting scene, he kicks the last one into the pole of a streetlight. When the agent falls to the ground, he moves his arms from a position where he could brace his fall to one where he could protect his face from the shattered glass that comes directly after when the glass from the streetlight falls and breaks in front of him. (00:09:10 - 00:10:00)
Continuity mistake: At the very beginning of the film when the 3 agents burst through the door where the captains are holding the meeting, if you notice the 3 agents enter the room and stop just after the broken door, and when the agent closest to Neo says, "only human," the other two agents are now a lot further in the room, there is no time to move forward as it is between shots this happens. (00:09:25)
Revealing mistake: When Neo fights the Agents near the beginning, he knocks out the first by knocking him into the wall. He then knocks the second into the wall by spinning round on the third Agent's back. After the shot of the second Agent hitting the wall both Neo and the Agent go from standing completely still displaying a clear "Action" cue. (00:10:00)
Continuity mistake: Near the beginning of the film in the big cave in Zion, we see Neo walk up to Trinity. As they kiss, Trinity's right hand is on Neo's neck. The following shot she has her left hand on Neo's neck. (00:26:40)
Continuity mistake: When Neo goes to see the Oracle he first encounters Seraph. In the middle of their fight scene in one shot you can see that Seraph isn't wearing his sunglasses despite in all other shots wearing them. (00:40:15)
Continuity mistake: In the scene where Neo meets the Oracle before the Burly Brawl, just after Neo looks at Seraph and says "so's he", from behind she is leaning her head on her hand, with her hand by her jaw. Then when we see her from the front (instant cut, no time she's not visible), her hand is against her temple when she says "keep going". (00:43:20)
Continuity mistake: In the scene just before the big 100 Agent Smith's fight, we see Neo and the Oracle talking on a bench. In one shot we see that the Oracle has her arm on the bench's back, then in the following shot we see her put her arm down by her side or on her lap, then in the following shot after this its back on the back of the bench. (00:45:10)
Continuity mistake: In the scene when Neo is talking to the Oracle on the bench, the Oracle is sucking on a sweet large enough to cause a bulge in her cheek. Whilst they are having the conversation, the camera obviously changes to whoever is talking. Neo gives a short response and then the Oracle replies straight away - no sweet. (00:46:15)
Continuity mistake: In the scene where Neo converses with the Oracle, there is the shot where Seraph reminds the Oracle that they should leave. Now you see that when the Oracle gets up, Seraph starts checking the area in front of the bench, looking away from Neo and the Oracle. But in the next shot with all three of them in frame, he is looking directly at Neo while the Oracle moves forward to pat Neo in the stomach. (00:50:25)
Visible crew/equipment: During the scene where Neo is talking to Agent Smith in the park area where Neo was talking to the Oracle, there is a close-up on Agent Smith's face. In his sunglasses you can see a bright white screen to reflect the light onto the faces of the actors. This isn't visible in any non-reflected angles. You can also see the cameraman on the other side. (00:51:15)
Continuity mistake: In the Burly Brawl scene towards the begining there is a birds-eye shot of Neo fighting four Smiths in front of him while moving backwards. He continues moving backwards and is hit. Just before the shot changes he is standing on a drain but when the shot does change he is about 3 feet in front of it. (00:51:40)
Continuity mistake: At the start of the Burly Brawl when we see Smith throw Neo through a bench, when Smith goes up to jump on him, from this point of view, the two or three steps behind the bench are nowhere to be seen, yet when Smith lands on the ground, the steps are probably less than a foot away from the bench. (00:52:30)
Continuity mistake: DVD version. In the 100 Smiths scene, a woman enters the courtyard and drops a shopping bag. The first shot shows two tomatoes falling out, one hurtling toward the camera out of the shot and a small box falling out of the bag. In the next shot of the ground, you can see several tomatoes and the box is back in the bag. (00:52:55)
Revealing mistake: In the 100 Agent Smith fight, you can see (especially in the larger shots) that there are many Smiths that don't look like Smith at all. Also, for the ones that have Smiths face digitally painted on them, when they turn around you can see that the backs of their heads are all different. (00:55:50)
Revealing mistake: In the scene where Neo is fighting the 100 Smiths, there's a shot of Neo baseball-smacking a Smith into a set of windows. While the scene is a bit blurry, it's pretty apparent that the Smith literally falls apart when he hits the window, like he was made of sausage links. (00:57:15)
Continuity mistake: When Neo Trinity and Morpheus go to visit the Merovingian in his restaurant, as the camera pans up the distance between the Merovingian and his girlfriend changes between shots. (01:01:15)
Continuity mistake: Near the middle of the film when Neo, Trinity and Morpheus are talking with the Merovingian, you see that the Merovingian is holding a glass on the table with his right hand, the glass is barely half full/half empty, yet in the following shot the glass has filled itself up a bit. (01:01:45)
Answer: This was made just for the trailers. The same part (without the Matrix code) can be seen when Smith says "suprised to see me?" to which Neo replies "No." and puts on his sunglasses before the Burly Brawl.