Plot hole: Suzie pulls out some of her teeth with a pair of heavy pliers. This would leave conspicuous tool marks on the teeth that would be visible to the naked eye, let alone under forensic examination. The conclusion would be that Suzie is missing, not dead, and the whole plot would unravel from there.
Plot hole: The first time they communicate with the "entity" in the spaceship, they find a correspondence between numbers sent by the entity and letters of the alphabet. The entity presents itself as "Jerry". Later on, the entity tells Dustin Hoffman, "Stop calling me Jerry" - and then Dustin Hoffman realizes that the number-letter correspondence was wrong, and the actual name of the entity was "Harry". But if that is true, how could they have communicated without problems before? The very first word that the entity used was "hello", which would have to be displayed wrong, since it begins with an "h" and has an "e".
Plot hole: During the end the murderer is thrown out the front window of the building. The students leave the building through the front door, but yet there is no body, and that doesn't seem to bother them!
Plot hole: The original ending planned was a massive tropical storm/water based chase scene. However, this was decided to be too expensive, and was switched for a cheaper, and some say weaker ending. Nonetheless, in Nicholas Cage's final speech, he says "I keep thinking about that tunnel, and what would have happened if I'd drowned." This makes no sense, given that in the new ending he came nowhere near a tunnel or drowning.
Plot hole: In the lobby of police headquarters, Danny Roman's lawyer tells him to make a deal with the prosecution. Danny turns to his wife Karen and tells her to wait in the car and he will be right back. Then he proceeds to go upstairs and overtake Niebaum's office. Much later when Chris Sabian is negotiating, Karen arrives on the scene wondering what's going on. How long was she waiting in the car? (00:28:35)
Suggested correction: This isn't a mistake. Karen (and anyone else still on the property) would have been sent away by the police once they became aware of the hostage incident. She went home to wait for Danny because she doesn't know he is the perpetrator. When she is called back to the scene by Sabian she wonders what is going on because she doesn't know that Danny has taken hostages in the building.
So she drove there with him and then just leaves him there? Lol. Can't see her just leaving without him since they drove there together. Even if people went around telling everyone to leave the area, I just can't see her not hanging around and waiting for him.
Plot hole: If Marybeth was able to seal her nostrils and use her extended finger to remove the cap and make nobody suspicious about her, why didn't Delilah do the same thing? She was alien, so she should've still been able to do it, same as Marybeth.
Plot hole: During David Leigh's narrative about Jim's court case, you are shown a number of newspaper headlines concerning the murders. One shows a shot of Locus looking at camera, with the caption 'Did Locus see his killer?' That shot was on the missing film which was found by David Leigh AFTER the murders were forgotten. So how did the paper get the picture?
Plot hole: Marion rips the paper into pieces and flushes them down the toilet. We see all the paper go into the toilet. Later when Lila lifts the toilet seat, there's one piece conveniently placed under the seat that couldn't have gotten there.