Continuity mistake: At the beginning of the big chase scene we see Trinity, Morpheus and the Keymaker in a car going down a street. If you look out the front in one of the shots, they are nearly at the end of the street. A few seconds later they are approaching the end of the street again. (01:19:55)
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)
Continuity mistake: The tire on the front wheel of Trinity's Ducati 996 changes from slick to treaded a couple of times between shots.
Continuity mistake: In the scene where Neo meets the Oracle, when Neo and Seraph are in the corridor with all the back doors, the small piece of wall around the door is white. However, when Seraph opens the door so that he and the Oracle can go through it, the borders of the door opposite to the open one are green.
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)
Continuity mistake: The door which is held open by one of the Twins gets splattered with blood on the inside when Trinity shoots at his arm. However, when Neo later runs towards the door before bashing it in, the splatter is gone.
Continuity mistake: When we see Neo stop all the bullets that the Merovingian's henchmen have just fired at him, Neo proceeds to let them drop on the floor where they are clearly visible. Yet just seconds later when all the Merovingian's men come running at him the bullets have all disappeared. (01:13:35)
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: When the 2 cops are being morphed into at the beginning of the highway scene, the driver is looking to his right while being morphed, but in the immediate shot, he is looking to his left, there isn't enough time in between shots for him to look the other way.
Continuity mistake: When the Tahoe is getting hit and crashed it loses its passenger mirror. When the Tahoe is hit by the other drivers the mirror is back on.
Continuity mistake: In the scene right before the freeway scene, in the city streets, the Escalade EXT rams a brown BMW 7-series in the purwuit of the Silver CTS. The BMW rips in half, but there's not a scratch on the EXT. Later in the freeway scene, you see a headlight blown out, and a katana sword can rip it, whereas a car smash causes no damage.
Continuity mistake: In the freeway chase scene when the Cadillac is being side-smashed by the police cruiser, the agent driving the cruiser disappears from the car when the vehicle hits the water barriers. It can't just be that he changed to a different body - that would have left the original occupant still in the car. (01:28:35)
Continuity mistake: When Trinity is driving through the tunnel leading up to the highway, the action goes into slow motion and Morpheus shoots out the Albino Twins' Escalade SUV driver side mirror to pieces. In the scene where one of the Albino Twins morphs back inside the Escalade SUV on the highway, in which they say "We are getting aggravated", "Yes we are", you see the full driver side mirror intact. It is gone again in the next scenes showing the driver side mirror. (01:24:50 - 01:28:00)
Continuity mistake: In the freeway chase, Agent Johnson jumps from an overpass onto the top of the truck carrying Morpheus and the Keymaker. Just before the truck goes beneath the overpass, a freeway distances sign (Whipple Ave ½, Woodside Rd 1-½, Marsh Road 3-¾) is briefly visible. As the truck emerges on the other side, the same sign appears again, behind Johnson, to the right.
Continuity mistake: In the freeway chase scene, look carefully at the Ducati carrier truck. After the truck's driver's body is taken over by one of the Agents and the camera shows the outside of the truck, you can see that it is a completely different truck, carrying a red shipping container instead of the motorbikes.
Continuity mistake: When Neo is talking to the Oracle, in the close up shots of her, her temple is resting on her fist. On the shot behind, her fist is on her cheek.
Continuity mistake: During the highway chase, just before one of the twins ghosts into Trinity's car, during the shot with the flipping car, the traffic behind Trinity's car is missing.
Continuity mistake: On the highway, while Trinity jumps from the trailer on the motorbike, the sun changes between shots.
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