Continuity mistake: During the final battle between Boone and Decker, at one point, they are wrestling on a wooden bridge, and the board beneath Boone's head breaks in half and falls into the cavern below. (It is even highlighted in a very dramatic shot looking downwards over the whole cavern as it falls) Yet, a few shots later, the board has suddenly re-appeared beneath his head, unbroken.
Audio problem: This problem exists in the extended Director's Cut. When Narcisse is first introduced in the hospital, when we cut outside to Decker and the police walking to the room, they suddenly hear Narcisse grunting which makes them rush to his room. However, they are quite the distance from his room, and Narcisse's grunts are fairly low, so it's obvious they shouldn't have heard him from that distance. The audio mixing tries to make his grunts sound louder, but it doesn't sound right at all... they're way down the hall from the room, but his low grunts sound like they're coming directly right next to them. This is all the more confusing, as in the theatrical edition, they are alerted to a distant scream by a nurse, which was much more believable. (As the Director's Cut is currently the most readily-available version of the film on Blu-Ray online, and is the director's intended edition, I believe it should count as a mistake).
Continuity mistake: When Decker is introduced killing the family, watch carefully when the mother falls over. There's a very quick insert-shot of what appears to be blood-covered fruit (or something similar) rolling away, leaving streaks of blood across the ground. However, she wasn't holding any fruit, nor was there enough time in between edits for her to have dripped blood onto fruit and then knocked them over. Obviously the product of a few shots being cut for pacing, but a mistake nonetheless.
Continuity mistake: As the police are seen prepping for battle, and Eigerman is delivering the line "Whether it be freaks, commies or third-world y-chromosome mutants we are there - the sons of the free", watch his hands as he picks up the large gun. As the camera cuts during the dialog, his hands have suddenly swapped positions on the gun.
Revealing mistake: During the big final fight at Midian, at one point, one of the men with a flamethrower accidentally stumbles backwards into a patch of burning shrubs/plants, which sets him on fire and eventually causes his flamethrower tank to explode. As he accidentally stumbles back into the shrubs, watch closely- one of the plants starts to fall over, and is attached to a small square board hidden in the dirt below that becomes visible, revealing that the plants were pieces of set-dressing.
Continuity mistake: During the final fight between Boone and Decker, right before he is killed, Decker almost falls backwards off a small "cliff", only to be caught by Boone. Watch the shots closely. In the first shot from above, he teeters on the edge, about to fall, and Boone isn't holding him. Yet in the next shot from below (looking upwards), Boone is holding onto Decker's shirt/jacket. The camera cuts back up above, and Boone is no longer holding Decker, but instead grabs him while shouting "Not yet!"