Plot hole: The scheme to lead a blindfolded Max and 99 to what they think is the airport via an illusion room would not work the way they do it. Since the base is underground, there is no way that what they did to represent ascending to ground level that would make a person think they were above ground.
Revealing mistake: When Max, the Chief and 99 are going through the wreckage, Max picks up solid wood that's obviously polystyrene.
Continuity mistake: At the car wash, the KAOS man drives his car in and there are two people in it for some reason, but when he gets out, he's the only one there.
Revealing mistake: The lift for going in and out of the KAOS base is meant to be sturdy metal, but it wobbles like a prop when the KAOS agent drives off it.
Continuity mistake: During one scene in the fake plane going off, a KAOS thug standing in the background has a shadow that magically moves between shots.
Other mistake: During the scene in the prison cell, the first shot has a hair sticking to the bottom right of the screen the entire time.
Other mistake: In one of the car wash fight scenes, two men accidentally kill one another. According to the angle of one of the guns, you can kill someone without actually hitting them.
Continuity mistake: In one shot, both Max and the guy holding him at gunpoint are covered in soap suds, but the next shot shows that only Max is covered.