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.
Revealing mistake: After the twins shoot the black Oldsmobile, it hits a barrier and does a spiral, and lands on its roof. That's impossible because the car's fender would have been torn off. It would have skidded a sharp right and went under the semi that Trinity was driving by. That indicates that there was a ramp to lift the car off the ground and do the spiral.
Deliberate mistake: In the scene where Neo is sitting with the oracle and talking, there is one quick shot of the fence area where Smith comes in. In spraypaint on the metal fence it has "ONE" written across it diagonally up to the right. When the oracle leaves and Agent Smith comes through the fence entrance the spraypainted "ONE" has disappeared.
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.
Revealing mistake: When the Keymaker closes the door with the Smiths firing at him, if you play it slowly you can see that no bullets actually hit him, as they would have caused bullet holes and blood stains, but his shirt stays perfectly fine right up to when he shuts the door.
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)
Revealing mistake: During the highway chase scene, when one of the twin is trying to kill Morpheus, one of the agents jumps on a car. There's nobody in the driver's seat. (01:27:00)
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.
Audio problem: After the Keymaker has been shot, Morpheus and Neo rush to him and turn him over. The Keymaker's gasping for air is very audible, but the first reflection of him that we see in Morpheus's sunglasses shows that his mouth is tightly closed. This is only visible in that one reflection shot. (01:49:00)
Factual error: In the freeway chase, when the agent tears off the car roof, it is seen as a floppy metal sheet. A roof is actually quite thick, supporting part of the car's structure, a built-in roll-cage, and of course the headlining. However, all of these things are nowhere to be seen.
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)
Visible crew/equipment: You can see camera equipment in the reflection of the sunglasses on the agent that takes over the tractor-trailer truck. (01:35:50)
Revealing mistake: When Smith is talking to Neo in the park after seeing the oracle, the direction of the sunlight over Smith doesn't match the shadows in the park.
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