Plot hole: The spinosaurus manages to smash through a metal reinforced wall designed to stop dinosaurs getting past it without too much effort, yet it can't get through a wooden gate secured by some metal bars. It makes no sense.
Plot hole: When the film opens, Jason is bound and restrained in an empty room. After killing the six security guards and appearing in the hallway, he chases after Rowan with a machete. Where'd he get this? All the guards had guns, and the rest of the room was completely barren. [Apparently, there was a cut scene (unfortunately deleted scenes weren't included on the DVD) showing Rowan with a box of Crystal Lake newspaper clippings and other Jason material/evidence, and his machete was one of the items in the box. Still a mistake due to the empty room (ropey editing), but that's the reason.] (00:06:00)
Plot hole: When the survivors first make an attempt to break out towards the station they kill numerous assailants at close quarters and yet only one of them (Uno) is infected. There must be dozens of the parasites floating around, enough to infect them all.
Plot hole: Why did the killer cut off the hot water? Did he think that Dorothy would come down and turn it back on herself with all those staff members in the house?
Plot hole: Early in the film, we learn that the former prostitute Annie Crook is married to and has an infant daughter (Alice) with Prince Edward Albert Victor. Secretly outraged, Queen Victoria dispatches various high-ranking operatives to eliminate this potential royal scandal. To that end, Prince Edward Albert Victor is secreted away, and his wife Annie Crook is kidnapped and barbarically lobotomized. We then learn that he baby, Alice (who was fortunately in the care of two other prostitutes at the time of the kidnapping), was sent to live with the parents of Annie Crook, no doubt saving the baby's life. That is the last time we hear of baby Alice until near the end of the film, where we are puzzled to learn that Alice was not sent to live with her grandparents at all, as stated earlier. Rather, the prostitute Mary Kelly took baby Alice away from an orphanage to raise as her own. No explanation is offered for this discrepancy.