Continuity mistake: During the freeway scenes, the katana Morpheus used as a foot hold to grab the keymaker keeps moving. It was at arm's length from the top when he inserted it; when Morpheus was standing on it, the sword was a whole body length below the top; when Morpheus took the sword out in his fight against the agent, it was back in its original position.
Continuity mistake: In the car chase scene, when Trinity is driving the cadillac, the Agent in the cop car slams into the driver's side of Trinity's car and the driver's side mirror is bent inwards. When Trinity drives the cadillac onto the exit ramp, the driver's side mirror is back in its normal position.
Continuity mistake: In the highway chase scene there is a shot of the police cars before they get onto the highway and the cars are Chevrolet Caprices. When they are on the highway chasing Trinity's car, the police cars become brand new Chevrolet Impalas. But when the police cars start to ram her, they become Caprices again.
Continuity mistake: When Neo and the keeper are fighting on the middle bench, one by one the bowls get knocked off - the two on the far corners (left and right) reappear and disappear at least once. Likewise the pot on the right hand table with stick-like things in - that table's completely cleared at one point, but that pot reappears.
Continuity mistake: During the freeway chase scene the Cadillac gets slammed up against the wall and sparks start shooting from the side to show that the car is being scraped by the wall. However, in several quick shots after we see the car gets scraped against the wall, there are only bullet holes and no trace of scraping against the side of the car. (01:28:30)
Continuity mistake: Further to the comment about some of the Smith clones not having Hugo Weaving's face pasted onto them, just after Neo does his back flip into two agents whilst kicking the two either side of him, just after he turns back around towards the camera, there is a very obvious stuntman standing just behind him who looks absolutely nothing like Agent Smith.
Continuity mistake: When the twin leaves the car that Trinity is driving, he is standing on the freeway by himself. You see a flat-bed truck, then a police car, then a red van pass him by. But when they show the shot ahead of him, the truck is still there, but the cop car and the red van are nowhere to be seen.
Continuity mistake: In the scene where Neo fights the Merovingian's henchmen he plunges a sword into one of them and pushes him off the balcony and jumps with him. The body falls near an already dead henchman. In the next shot when the others jump off the balcony the body with the sword is away from the first body. (01:16:00)
Continuity mistake: In the car chase scene when the Twin enters the car with Morpheus, Trinity and the keymaker the camera view changes between aerial shots and shots from in the car. In the aerial shots the road behind them is completely empty. From the shots in the car you can see several cars behind them through the windows.
Continuity mistake: In the scene of the freeway chase, where Trinity, Morpheus and the Keymaker are in one car on the right side of the freeway, there's a shot from the car of the Twins (two or three lanes to the left), Trinity's car passes a truck, when the car appears again ahead of the truck there is only the driver inside the car, no passengers.
Continuity mistake: As Morpheus walks away from the wrecked car, the position of his right hand, clenched with index finger pointing straight downwards, would indicate he is gripping his pistol. Yet in the next cut to a view from behind him his right hand is empty. The pacing of the sequence suggest he wouldn't have had time to holster it, yet we see him produce it from behind his back after he has sliced the twins' car. (01:25:40)
Continuity mistake: In the Burly Brawl scene towards the begining there is a birds-eye shot of Neo fighting four Smiths in front of him while moving backwards. He continues moving backwards and is hit. Just before the shot changes he is standing on a drain but when the shot does change he is about 3 feet in front of it. (00:51:40)
Continuity mistake: In the shot taken above the Twin's right arm just before the SUV smashes the trunk off the BMW we see that Trinity's Cadillac already made a left turn and is about 70 feet away. In the shot made from inside the SUV just after hitting the BMW, the Cadillac is still taking the turn and seems stuck on the sidewalk. The SUV is about to pass it to the left. (01:20:10)
Continuity mistake: When Trinity is on the freeway and sees the motorbike truck from the bridge there are several cars either side of the truck travelling at the same speed. When they jump over,the top down view shows no cars and also the following shot from under the bridge shows no cars. (01:29:05)
Continuity mistake: In the scene where Trinity rides a motorcycle and is being chased by the police, we see the cop cars right behind her, almost nudging her back wheel. From behind her, she dodges a car, which crosses the road line and should stack right into the police car behind it, but escapes miraculously unscathed. (01:27:40)
Continuity mistake: In the scene where Neo meets the Oracle before the Burly Brawl, just after Neo looks at Seraph and says "so's he", from behind she is leaning her head on her hand, with her hand by her jaw. Then when we see her from the front (instant cut, no time she's not visible), her hand is against her temple when she says "keep going". (00:43:20)