Continuity: When Bane is talking to Neo while holding the knife to Trinity's throat, the blood appears and disappears on her throat.
Continuity: When Neo is talking to the Oracle the magnetic letters on the refrigerator behind him disappear then reappear.
Revealing mistakes: Obvious stunt double When Neo is punched into the wall by the train man.
Continuity: As the Hammer is reaching the gate to Zion, the hovercraft's gravity pads (glowing pods) switch between being damaged and fully functional. In addition, all of the aft pads were damaged at one point and the hovercraft was seen dragging the tail end on the tunnel. However, once the ship reached the gate, all pads, including the damaged rear pads, were shown to be fully functional.
Continuity: When Neo is talking to the Oracle, she sits down and slips her bracelet over her wrist. When we cut back to her, she puts on the bracelet again.
Continuity: When Seraph is trying to get out of the building with Sati, he takes her into a corridor, where the lights go out and they are left in pitch blackness. After trying a few doors in the dark hallway, he forces one open. We cut to a view inside the room they just burst into, and there is light in the corridor behind them.
Audio/visual unsynchronized: When Seraph and sati are looking for a place to hide from the Smiths, Seraph breaks in the door, he then swings the door closed and we see and hear it latch even though he just broke it.
Continuity: When the Logos passes above the cloud layer and the sun is visible forward from the cockpit, in the next shot, the moon is visible behind the Logos, but it is illuminated as if the sun was behind it.
Continuity: When Neo bids goodbye to Morpheus the plugs on the back of Neo's neck keep disappearing and reappearing.
Continuity: Agent Smith's tie knot changes during the beginning of the final fight.
Continuity: When Neo is lying in the crater during the final fight, one of his ears is filled with muddy water. In the next shot we see his other ear filled with water while the one which was previously filled is now empty.
Continuity: When Smith and Neo are running at each other in the rain for the final battle, the camera focuses behind their feet in slow motion. You can visibly see both lines of Smiths on either side of the street. However, you cannot see their opponents, just the feet of whoever it is focusing on.
Continuity: When Trinity, Morpheus, and Seraph go to visit the Merovingian, the Merovingian is seen eating olives from his drink (a Martini). At first glance, there are only two olives. He takes half of a bite out of the first olive, then finishes it, then eats the second. However, just moments after eating the last olive, a third olive magically appears on the toothpick.
Crew or equipment visible: In the final battle in the crater, after Smith picks up Neo and punches him, you can see a wire just above Neo's right shoulder dragging him along the ground.
Continuity: In the train station scene the Train Man turns and fires. Seraph throws himself against the wall. When the camera cuts back Seraph throws himself against the wall again.
Errors made by characters (possibly deliberate errors by the filmmakers): When Neo is talking with the Oracle, he says "How did I stop four sentinels just by thinking it?", when in fact, at the end of The Matrix Reloaded (2003), we saw that there were actually five sentinels that Neo stopped, not four.