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: During the highway chase scene, when Trinity and the keymaker jump on the motorcycle truck, the bikes change between shots. Viewed from the side, from the front to the rear, there's a red, a black, and then three red bikes. When Trinity calls Link for a driving program, there's now a red, two blacks and two red bikes. (01:29:55)
Continuity mistake: During the Burly Brawl (Neo VS 100 Agent Smith clones), there is a point where dozens more 'clones' burst through the doors of two buildings. In one shot you can see that the number of clones simply ends, and no more are coming after a point (very briefly at the end of one of the first shots), but in the overhead shot shot, there are suddenly more and more Smiths pouring out at a constant rate. There is not even a pause in the Smiths coming out, so it makes no sense.
Continuity mistake: Right at the beginning of the fight between Morpheus and the Agent on top of the semi-truck, the Agent sends Morpheus sliding to the side of the trailor. In the first shot, Morpheus' left leg is over the edge, but in the next shot, his whole body is on the trailor and he has to turn to get close to the side.
Continuity mistake: In the freeway scene, Morpheus fights an agent. Right before Morpheus gets knock off onto Niobe's car, you see Morpheus land and lose his balance on the left side of the back of the truck, but when there is a shot of Morpheus falling off the truck, he is falling off the centre. (01:34:55)
Continuity mistake: In the car chase scene, just before they go onto the freeway, the twins fire a machine gun at them and make quite prominent dents on the top of the car. However, in the scenes that follow, the bullet holes are not there. This is most obvious when you see the car from the top and the black car next to it crashes into a barrier. They come back when an agent lands on the top of the car and rips it off.
Continuity mistake: Right before the Twin enters Trinity's car, he shoots a black car in front of them and then continues firing on Trinity and Morpheus. However, when the car is seen flipping in slow-motion, you can see bullets hit on the hood of Trinity's car up to the windshield and then instantaneously go to the roof.
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)