Plot hole: In the end of the film it is heard the police want to exhume the body of Charles Lee Ray from his grave site in New Jersey. Now when Chucky and the crew get to the grave site they find and kill a coroner who is digging up the body. He is the only one there at 1am, by himself, a lonely coroner without any police officers, after all this is a police investigation and I doubt the cops would have him there alone. Then right at the end the Detective who is hunting them arrives. Now he is a cop from Lockport, about six states away. A. Why did he drive all that way to see the body? B. A cop from all the way down there shows up but no new Jersey cops are at the scene?
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: In the scene where Katrina is watching through Valek's eyes as he kills father Molina, Crow orders father Giteau to "find out where an old padre is missing". But Katrina never described father Molina, all she said was "He killed the priest". Crow could not have known the age of the man who was killed.
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: The rape scene in the parking lot... there is no one around for THAT long? But wait, once the detectives come in the scene two people are walking in the background with a shopping cart - they must have seen something!
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: At the end of the film all the police and ambulance vehicles manage to get into the school, but earlier Keri/Laurie smashed the mechanism that opens the gate.
Suggested correction: There's been a series of murders tied to an infamous serial killer... more than likely the police broke down the gate to gain access. (Which can be done in any number of ways: sawing through the locks, having the fire department dismantle it, ramming through it with an armored vehicle, etc.) They're not going to not come in just because there's a gate they can't open. Also, a quick Google search indicates that often, police are given access codes or ways to remotely open gates at certain buildings (schools, senior centers, etc.) in the event of an emergency. So it's entirely possible they also had a way to open the gate without breaking it down.
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.