Continuity mistake: In the fight scene between Seraph and Neo, items on the tables are constantly being knocked off and reappearing. In the first long shot, where Seraph and Neo jump from the rightmost table to the one adjacent, a bottle is knocked off, and then reappears. Almost immediately after, during an overhead shot, Seraph knocks one of the flat ashtray-like containers off the table. He moves back, obscuring the place where it was. When he moves forward again, it's back on the table.
Continuity mistake: DVD: In the 100 Smiths brawl, Neo dives backwards about four feet from the ground and a Smith dives at him from the ground to Neo's left. The following shot shows both of them at about twenty feet in the air and it looks like they are descending from the fourth floor of the building in the background.
Continuity mistake: In the scene where Neo converses with the Oracle, there is the shot where Seraph reminds the Oracle that they should leave. Now you see that when the Oracle gets up, Seraph starts checking the area in front of the bench, looking away from Neo and the Oracle. But in the next shot with all three of them in frame, he is looking directly at Neo while the Oracle moves forward to pat Neo in the stomach. (00:50:25)
Continuity mistake: After one of the agents rips the roof off the car on the expressway, there are some shots that show the interior of the vehicle still dark as if the roof were still intact.
Continuity mistake: The wound and the sleeve of the jacket on Trinity's arm changes after she's cut by one of the twins. When she's cut, the wound and rip in the jacket are thin and diagonal. As Morpheus is calling Link, the wound is not really visible and the cut in the jacket is now larger and squarer, and has changed direction on her arm. (01:21:00 - 01:22:50)
Continuity mistake: In the scene where Trinity, Morpheus, and the Keymaker are standing on the bridge, Morpheus says "Trinity, get him out of here." Trinity then grabs the Keymaker and they both jump off of the bridge onto a truck. Then, when the car the twins are riding is heading toward Morpheus, you can see that there are guard rails on both sides of the bridge, however, next when Morpheus cuts the tires on the car the twins are riding with his Katana, the camera cuts a side shot of the bridge, and one side of the guard rails on the bridge has mysteriously disappeared. (01:29:30)
Continuity mistake: During the freeway scene, the Twin shoots a black car directly in front of Trinity's car. He shoots on the hood and then a trail of holes are seen going up the windshield. The next shot is one from inside Trinity's car between Trinity and Morpheus, but no bullet holes are in the car ahead.
Continuity mistake: DVD version. In the 100 Smiths scene, a woman enters the courtyard and drops a shopping bag. The first shot shows two tomatoes falling out, one hurtling toward the camera out of the shot and a small box falling out of the bag. In the next shot of the ground, you can see several tomatoes and the box is back in the bag. (00:52:55)
Continuity mistake: When the Keymaker opens the door inside the white corridor near the end, you see in the reflection on the doorknob and it shows the corridor, but it does not have any doors in the reflection and there is a white door behind the Keymaker, which you cannot see otherwise when you look in that direction.