Plot hole: So he needed the help of a big strong burly guy to flip the safe with the body, end over end to the pit, but he somehow was able to easily get it out of his basement and into the back of his car by himself?
Plot hole: With people around the world turned into zombies, there is no way to maintain power plants, thus no lights should be lit, not to mention the functionality of an amusement park.
Suggested correction: The sequel film gives this a (very flimsy) justification, saying that everything runs on power from dams. Stupid, but at least trying to explain things.
Plot hole: When Abby and her kids are abducted, the sheriff is sitting right outside her house and sees this happening. Yet the video didn't record. Well the sheriff saw it all with his own eyes so why wouldn't his testimony hold up? The tape actually shows the UFO so there's proof right there. (01:08:55)
Plot hole: When the 3 criminals are in the kitchen with Mary's parents, you see a picture of Mary on the fridge. There's no way none of them didn't see it considering they were in the kitchen for an extended period of time.
Plot hole: At the beginning there is an audio recording of Thomas talking to the police. He explicitly says 'They killed her! They Killed my sister, my mom!' or something to that effect and that Thomas was arrested for the rape and murder of his sister and he killed himself in custody. At the end, his sister is killed and the little epilogue says that the sister's body was found in her brother's arms and when their mother found out about the 'death of her children' she killed herself. That doesn't make sense logically. Thomas was alive when his mother was dead, according to the clip at the beginning.
Plot hole: If the missing people were already in that cave, then why did they have to cut locks of the building and pry boards off the hole?
Plot hole: Every ghost that we see in the house looks the way they did when they died, for example the girl from the film's intro is seen without skin on her face, which happened to her before she died. However, in the final scene when we see Simon's ghost joining them, he looks completely normal, when he should have had a throat slit wound and the carved markings on his skin. (01:31:20)
Plot hole: During Ed's transformation back to humanity, he burst into flames several times. His heartbeat was monitored using wires attached to his chest. They did not stop working despite being in the flames.