Plot hole: Andy is suspected of having killed Eddie Caputo, because he was at the scene when Eddie's house blew up and Eddie was killed. But there are glaring things that go unquestioned: None of the cops seem to think it's strange that a six-year-old kid would travel by himself so far to some random house in order to blow it up. The South Side neighborhood where Eddie lives is halfway across the city from Andy's apartment. How did Andy know where Eddie lived? How do the cops think he even knew Eddie at all? None of them address this most puzzling problem.
Suggested correction: The police believe Andy to be insane (hence why he is sent to a mental institution instead of juvenile hall), and thus do not believe his choice of victims to be in any way rational.
Also, as unlikely as it is that a six-year-old child could (or would) travel halfway across the city to murder a random person, the possibility that a child's doll came to life and carried out the act was considered far too outlandish at that point in the plot.
Suggested correction: We don't see the entire investigation. We just see the cops holding Andy then taking him to a psychiatric clinic. Chances are they were asking those questions and we just didn't see it because it's not important to the plot. Regardless, the cops have every reason to believe Andy either knows about or was partly responsible for the murders considering he keeps showing up at murder scenes. There's only so many conclusions you can draw, even if they don't make sense.
Plot hole: When the deputy arrives at the sheriff's house, Michael gets out and leaves the door open. The deputy comes out to the car and sees it open. And he thinks nothing of it, despite knowing he didn't open it. Logic would say, "Well someone else opened it."
Plot hole: When the policeman asks Kirsty at the beginning who came when she solved the box she says the Cenobites; she had no way of knowing what they were called. Frank only told Julia; Kirsty didn't hear it anywhere and the Cenobites themselves didn't tell her either.
Plot hole: After Dennis (the first guard assistant) gets killed, the vault is open for several minutes before the old guard arrives. The hobgoblins, however, do not run for their freedom, but patiently wait until the hero, Kevin, comes in a later scene and opens the door. Then they escape as quickly as they can.
Plot hole: When Debbie and Mike are in the pink cocoon room of the circus tent Mike yells, 'Joe Lombardo.' However, Joe Lombardo doesn't die until at least 4 scenes later in the movie, when a Killer Klown edges him off the road and over a cliff.
Plot hole: Freddy is killed at the end because he sees his own reflection in a mirror, which causes the souls in his body to revolt and kill him. But this weakness to mirrors and reflections doesn't fit in any other film of the series. He repeatedly appears in mirrors in the other films, and in the climax of "Dream Warriors," he even appears in a hallway of mirrors that are facing each other, where he would have seen his own reflection multiple times. No matter how you slice it, his death in this movie doesn't add up in the overall context of the series.
Suggested correction: It's implied that it's not looking in the mirror that kills Freddy, but some extension of Alice's Dream Master powers. Both her and Freddy's powers have been changing and fluctuating throughout the film. It's not really explained, but it doesn't contradict previous films.
Plot hole: When the old women are painting the eggs, you can see them blowing the yolk out of some. Why didn't they blow the yolk out of the Critter eggs?
Plot hole: When James and Gemma arrive back at the waxwork just before the film's climax, they claim a "man with a high-pitched voice" (Hans) invited them. In the earlier scene when they decided to not enter the waxwork, they left before Hans answered the door, and he couldn't have found their phone numbers anyway.
Plot hole: In part 6, Jason kills numerous people as well as the entire sheriff's department (minus 1) yet investigators just leave his body in the lake and not recover it? Very unlikely.
Plot hole: It is explained that due to the severe beating/stabbing Cordell received in prison, he has no "higher brain function." How does this make him impervious to gunshots?
