Continuity mistake: Near the beginning of the freeway chase scene, we see the twins take aim at a gold Chevy SUV. First of all, the first head on view we see of the SUV it has it's Daytime Running Lights on, the next time we see this view they are off. Secondly, one twin shoots out the passenger window and completely shatters it, however after the scene cuts briefly back to the twin it returns to the SUV just as it begins to flip and we see the window shatter yet again. (01:22:05)
Continuity mistake: When Trinity is driving down the freeway, the bullet holes in the right side of the car are not there on several occasions when the car comes into view from behind other vehicles.
Continuity mistake: In the highway scene when Trinity steals the bike from the truck, you can see that the bike's tires are completely clean while the bike is in the air and in the next shot just before the bike touches ground the tires are now all dirty.
Continuity mistake: When Morpheus rolls out of the way of the Twins' car you can see his smoking, bullet-ridden car in the background. The door's wide open when he rolls, and a split second later when he slashes their car, the door's almost shut. No-one's anywhere near it. (01:25:45)
Continuity mistake: In the freeway chase scene just before the two trucks collide, Morpheus and the Keymaker are at the front of the white truck (you can tell because otherwise you wouldn't be able to see that much of them in the final front shot), but when they're catapulted forward they're right at the back.
Continuity mistake: In the fight scene in the mansion, when Neo stabs the guy's hand with a sai, his hand is in the top part of it, but when the shot cuts his hand's now a) in the bottom half, and b) free of the sai anyway - he's just gripping the sword which is in the bottom half, with nothing trapping him. (01:15:20)
Revealing mistake: On the freeway scene, there are many cars and trucks that were computer generated to fill in the road, but the shadows are just under the vehicles, not angled away like on the real ones.
Continuity mistake: In the freeway chase scene, when the agent jumps on the intermediate car, it flips over. During the second slow-mo shot of it tumbling end over end, a bent piece of the bumper can be seen to leap UP from the ground, become un-bent, and attach itself back onto the car. This process is also visible for several other small pieces of debris on the road. It is NOT simply broken glass bouncing upwards - the bent bumper reassembles as it leaps up, and small metal shards suddenly go from motionless to flying towards the car. Broken glass moves as it would be expected to: away. It seems that the glass may have been edited in later.
Continuity mistake: In the scene where Trinity is typing the 'disable grid nodes 21 - 48' command, she is pressing random keys rather than the correct sequence. The text already on the screen in the beginning of the next shot is 'disable grid,' but the 'G' key is one of those that have not been pressed, whereas 'H', for obscure reasons, has been. (01:43:35)
Revealing mistake: During the freeway chase there is a shot over the shoulder of one of the twins as he shoots at our hero's car. He rakes his stream of bullets from left to right following the car as it passes behind a white truck - notice, however, that there are already bullet holes in the truck before the stream of bullets ever reaches it. (01:25:45)
Continuity mistake: Right before the highway chase scene, when the Key maker says, "Always another way", if you look at his head, he has a full head of hair. When Trinity and the Keymaker jump off the bridge onto the motorcycle truck, you can see the Keymaker has a bald spot and a little less hair.
Visible crew/equipment: After the BIG crash during the freeway scene, if you look closely from Trinity's Ducati you can see the paramedics, cameramen, and equipment.
Revealing mistake: In the freeway chase scene, the black car that gets shot at by one of the twins and flips over the k rail and over the Cadillac has skid plates under the nose, so as to slide and flip the k rails easier. (01:26:00 - 01:27:20)
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)
Deliberate mistake: In the scene where Trinity jumps out the building with machine guns and an agent right behind her, we see that while they are exchanging bullets, her hair is slick back and wet. But once she is shot and falling down freely, her hair is dry and flying freely.
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.
Revealing mistake: Just as Neo begins fighting in the "Burly Brawl," take a look at the Smith to the right of him (he puts his hand on Neo's shoulder I think). The face is not Hugo Weaving's but the face of the stunt person. Looks like the effects crew forgot to put Weaving's face on that guy.
Chosen answer: Obsolete programs are given the choice of deletion or exile. The Merovingian takes them in and, with his abilities to code the Matrix, allows them to stay under his protection.
Captain Defenestrator