Continuity mistake: Before Dana and Marty enter the control room and release all the monsters into the control centre, there is a thermos flask and a torch sitting next to each other on the control room's desk. But once they enter the control room, the position of the thermos flask and torch have changed without anyone touching them.
Plot hole: Marty Mikalski discovers a micro-camera in the cabin and is immediately grabbed by the cursed zombie Judah Bruckner, who drags Marty through the window and plants a machete in Marty's back. In that shot, the machete is obviously buried in Marty's back, which should have broken ribs both back and front, severed spinal nerves, penetrated arteries (as well as the right lung), and protruded from his chest. Marty was dead on arrival in that one stroke. Yet Marty emerges at the end of the film as the hero, with no gushing blood from his back or chest or mouth, and no explanation of how he miraculously removed the machete from his back.
Plot hole: When Dana realizes that the puppeteers made them choose their own deaths (while standing in front of Fornicus in the elevator) she does so by watching the puzzle ball he holds. But she never saw the puzzle ball back in the cellar. Only Curt handled it briefly and is shown approaching her without it when she starts reading the diary.