Other mistake: When the team descends to the bottom of a hole and one female member is first wounded and then dies. After checking her pulse, the others pronounce her dead and begin moving out. As the last one is leaving, the "dead" actress lifts her head up off the ground and looks left.
Revealing mistake: Hudgens starts screaming and grabbing for his chest long before Burke's knife hits him in the chest.
Continuity mistake: During the taxi chase at the beginning of the movie, the damage done to both cars changes between certain shots.
Continuity mistake: In the scene in the science lab, Hudgens shoots an agent then puts the key in the door. It cuts away and then back and the key has disappeared.
Continuity mistake: Near the beginning of the movie, during the taxi chase, the Ford Taurus taxi has no rear licence plate. After ramming the lead taxi a couple of times, and after turning down an alleyway, a shot from the rear shows the Taurus as now having a rear licence plate.
Plot hole: In the opening text scroll, it is said that the creatures live in the dark, and the name of the movie is "Alone in the Dark". But at the very end (when Edward and Aline are walking around the deserted city), the camera zooms in on the couple suddenly, implied they were attacked by one of the monsters, but in broad daylight.