Plot hole: In the end, when Charlie is advancing on Emily while turning his light on and off, the final time he turns it on, Kathrine is in front of Emily. How could she get there so fast without being heard? There's at least 4-5 inches of water that would make sneaking very hard.
Plot hole: The Hellworld website at the beginning of the film has eerie music and also Pinhead's voice reciting some of his famous lines from other Hellraiser movies, which is impossible; there's no way that someone could have gotten recordings of those moments in the past where he said the lines, so they couldn't be playing on an internet webpage.
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.
Plot hole: Tyler jumps into the water, then grabs his mask and puts it on and begins swimming, but he fails to clear his mask by blowing the water out of it. Without clearing it, he wouldn't have been able to see a thing.
Plot hole: Travis does the last time jump to change the events of a previous time jump. As all the jumps were to the exact same time to kill the same dinosaur, the travelers of the second jump must have found there the travelers of the first one. The travelers of the third jump must have found the travelers of the second and the first, and so on.
Plot hole: If the creatures are strong enough to simply burst through the walls, as shown at the end of the film, then the creature upstairs should not have been stopped by the small door that Bozo, the bartender and heroine shut on it to stop it. It was one of the larger creatures as well, so it could have easily gotten through.