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: During the freeway scenes, the katana Morpheus used as a foot hold to grab the keymaker keeps moving. It was at arm's length from the top when he inserted it; when Morpheus was standing on it, the sword was a whole body length below the top; when Morpheus took the sword out in his fight against the agent, it was back in its original position.
Continuity mistake: In the car chase scene, when Trinity is driving the cadillac, the Agent in the cop car slams into the driver's side of Trinity's car and the driver's side mirror is bent inwards. When Trinity drives the cadillac onto the exit ramp, the driver's side mirror is back in its normal position.
Continuity mistake: When Neo and the keeper are fighting on the middle bench, one by one the bowls get knocked off - the two on the far corners (left and right) reappear and disappear at least once. Likewise the pot on the right hand table with stick-like things in - that table's completely cleared at one point, but that pot reappears.
Factual error: In the scene where Neo is shot at by the French guy's henchmen, they shoot with different types of guns. 4 of these are submachine guns which would fire 9mm. Another is a M1928 Thompson would fire .45 APC. Lastly there is a Heckler and Koch G36K which would fire the drastically different 5.56x45mm NATO. When Neo stops the bullets, they are all 9mm Parabellum rounds.
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)
Deliberate mistake: When Morpheus is facing the twins' car, the road's not all that wide, and there are concrete barriers both sides of him. After he rolls to the side and slices their car, we see a side shot, quite far back from the road, and the barrier closest to the camera has disappeared (presumably so we get a better view). In a closer view, both barriers are back again. (01:29:25)
Continuity mistake: When the twin leaves the car that Trinity is driving, he is standing on the freeway by himself. You see a flat-bed truck, then a police car, then a red van pass him by. But when they show the shot ahead of him, the truck is still there, but the cop car and the red van are nowhere to be seen.
Continuity mistake: In the scene where Neo fights the Merovingian's henchmen he plunges a sword into one of them and pushes him off the balcony and jumps with him. The body falls near an already dead henchman. In the next shot when the others jump off the balcony the body with the sword is away from the first body. (01:16:00)
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: In the shot taken above the Twin's right arm just before the SUV smashes the trunk off the BMW we see that Trinity's Cadillac already made a left turn and is about 70 feet away. In the shot made from inside the SUV just after hitting the BMW, the Cadillac is still taking the turn and seems stuck on the sidewalk. The SUV is about to pass it to the left. (01:20:10)
Continuity mistake: When Trinity is on the freeway and sees the motorbike truck from the bridge there are several cars either side of the truck travelling at the same speed. When they jump over,the top down view shows no cars and also the following shot from under the bridge shows no cars. (01:29:05)
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)