Continuity mistake: Near the beginning when we see Neo walk into the room where the captains, Morpheus, Trinity, and the others are, if you look at Trinity she is standing behind Link in one shot, then he is standing behind her in another, and it is like this for several shots. (00:42:50)
Revealing mistake: When Neo and Smith are fighting at the end of the film - when Smith knocks Neo into the rafters of the room they are in, you can see Neo's face, and it's obviously Keanu Reeve's stunt double. (01:44:30)
Audio problem: As the trio break into the club, they take on some bouncers. One of them gets his gun turned on him by Trinity, pushed right into his chest - we hear two gunshots, with corresponding wounds, then a third shot which has no effect. (00:14:50)
Continuity mistake: During the big rain fight scene between Neo and Smith, Neo punches Smith, who flies into the road making a large dent/scrape. In the next shot, when they are flying above the road, the damage is nowhere to be seen. No other damage is repaired throughout this fight. (01:43:40)
Continuity mistake: In the scene where the "Smith infected" Bane has the scalpel to Trinity's neck, we first see Bane's head just right beside Trinity's lips (on the side). But in the next shot, Bane's head is way back near Trinity's neck still holding the scapel. (00:51:00)
Continuity mistake: In the final battle Neo/Smith scene, when Smith crashes Neo into the ground, the crash causes several cars to fly. When all the Smiths head to the hole to watch, the overturned cars are gone.
Revealing mistake: During the fight for the dock, after the first APU calls for a reload, Kid is seen in an ammo bay right before a fellow ammo runner is being sent out. As the door opens, a sentinel attacks them and all of them react surprised, except the ammo runner and the guy standing next to him, who don't react at all.
Continuity mistake: At the start, When they're running a search for Neo in the Matrix, Morpheus' arms keep switching. For example, in one of the closeups, his arms are by his side, when in the previous shot it's rested on his chin. And when that guy comes in and says 'Sir, I've got the projections,' his arms are folded.
Revealing mistake: When Neo kicks Smith through the window, if you look carefully you will see that it is a stunt double. (01:46:05)
Visible crew/equipment: When Smith and Neo are fighting in the building Smith is knocked to the floor. When he gets up you can see the stage light in his glasses. (01:44:35)
Revealing mistake: During the scene with Deus Ex Machina, see carefully the shot when Neo says "I won't" you will see two strange horizontal lines going down; visible specially on the left side of the screen. They are visible in the trailer too.
Continuity mistake: When Trinity, Morpheus and Seraph go to see the Merovingian in his club, there is a fight scene before they enter the club. When Trinity kicks the guy at the end of the fight scene, the guy has his arms by his side. In the following shot they are now outstretched. (00:17:00)
Continuity mistake: When the Logos plummets from the sky and crashes into the machine tower, Trinity is skewered with cables. In slo-mo you can see that at least two cables penetrate her upper chest, but when Neo is lying next to her a minute later the cables have impaled her below the ribcage and there are no chest wounds. (01:32:20 - 01:33:45)
Continuity mistake: In the final fight between Neo and Smith there is one shot of Smith's legs running towards Neo and one shot of Neo's legs running toward Smith. In those shots you can see that they are not running against each other.
Continuity mistake: When Neo wakes up in the station, he is sometimes right next to the edge of the platform and sometimes further from it. (00:04:10)
Continuity mistake: When Neo gets up in the final fighting scene with Smith after he says 'You're right Smith, you're always right,' his hair is pushed back from the rain and mud. In the next Neo shot, it's down over his forehead.
Continuity mistake: When the "Hammer" is being chased by the sentinels we have one shot of its captain in which he says:"Lock that down". When he says this he has some type of earphones, but in the next shot he doesn't has them any more. Between both shots the ship doesn't make any move that could make those earphones fall nor time for the captain to remove them.
Visible crew/equipment: In the Merovingian's club, when Morpheus knocks the girl back and shoots with her gun you can see the white lights/screens in his glasses. (00:16:10)
Factual error: The flight of the Hammer is a very bumpy one and more than once the ship is either upside down, on its side or straight up and down. The crew of the Hammer are completely unaffected by this and keep feeding ammunition to the guns. The Hammer's movements should be tossing them around since they aren't strapped to a chair like the pilots and the gunners are.
Visible crew/equipment: When Neo wakes up in the train station, Sati's dad tells her to, "Leave the poor man in peace." When she runs off, a piece of tape is visible at her feet, showing her where to stand. This is visible in many wide shots, but particularly in this shot.
Answer: In the first film she points this same sign out to Neo and explains that it means "Know Thyself"