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: 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: 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: When Morpheus faces the Twins' car with his katana, there is a shot from the side (the same shot where the side of the bridge disappears) where a part of the highway below is visible. It's completely empty while only seconds before you can see the highway full of cars.
Continuity mistake: Before the freeway chase and a little bit after they leave the garage, the twins shoot and crash the BMW, then Trinity's car turns right and drives off. In the next shot, the CTS is parked in the corner.
Continuity mistake: When Morpheus, Neo and Trinity arrive at the Merovingian's, the door keeper says "Follow me". The reflection in Morpheus' glasses shows the man still standing there, but in the next shot he has already started walking away. (01:03:30)
Continuity mistake: When Trinity and the Keymaker are on top of the motorbike truck there is a dark lorry which is seen to be behind the truck in the inside lane. Then in the close-up of the Keymaker when he holds the key up the truck is a lot closer to them. (01:26:30)
Continuity mistake: Right before the car chase when the car exits the garage the parking lights are on. Then it makes a right turn and one of the parking lights is out (The one on the passenger side). The next time you see the front of the car both lights are on.
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: 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 burly brawl, Neo gets tossed into a brick wall and gets dirt and concrete dust on his back. When he lands on the ground his back is suddenly clean.
Continuity mistake: In the corridor of many doors where Neo fights all the Smiths the two furthest Smiths draw their guns twice.
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)
Continuity mistake: When Neo is fighting the three agents, the glass of the streetlamp falls. When he flies off, the glass on the ground disappears. In the next shot, it reappears when the Agent Smiths are walking on it.
Continuity mistake: When the Merovingian's henchmen are shooting at Neo, a shot is shown from the side to show everyone firing their weapons. The man on the far left (the closest) makes the arm movements to indicate that his weapon is firing continuously, but his gun is only seen firing once.
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)
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.