Plot hole: When Toby is checking everyone to make sure their costumes work, wheelchair-bound Bud is shown standing in a coffin-fixture. Since he was in the coffin costume, there was nothing there to be "holding" the character in a standing position, and he was obviously not in his wheelchair, as he is at standing height with everyone else.
Plot hole: Cady's plan to get revenge on Bowden includes raping and assaulting Lori. This part of the plan, however, hinges on Lori not reporting Cady to the police, which he had no way of knowing that she wouldn't. If she reported him, the investigation would have created huge problems for Cady. He bit off a chunk of her face, so the wound could have been matched to his teeth, as well the chunk of skin he bit off and spit out most likely would have had traces of his saliva on it. Not to mention evidence that could have been gathered from a rape kit and eyewitnesses that could have placed Cady at the bar with Lori beforehand (the bartender, for example). In all likelihood, he would have been arrested, tried and convicted. Lucky for him, Lori was too ashamed to report the incident.
Suggested correction: Luck didn't come into it. Cady specifically targeted her because of her connection to Bowden, and took the calculated risk that she would not want her sexual history being dragged in front of a court and all her co-workers. This ties into Cady's motive for wanting revenge on Bowden in the first place, as he had suppressed similar evidence in Cady's original case. Also, Cady is a very unhinged individual; the submitter's opinion on how sensible his actions are does not make them a plot hole.
Plot hole: No amusement park ride company would ever produce a prop scythe that was as sharp as depicted in the movie.
Plot hole: The pipe bomb that Maggie uses to kill Freddy is the same one that was found in Spencer's room earlier in the film. It's already been established that Freddy was erasing the people he's been killing from existence, so that pipe bomb wouldn't be there to use on Freddy.
Plot hole: When Torch, Blade and Leech Woman go to the farmer and his wife's house while they are asleep, they killed both the farmer and his wife. The wife was consumed by flames, but not the farmer. When Torch and Blade returned to the Puppet Master with the brains, the Puppet Master says the brains are burnt up. The farmer's brain would not have been burnt up, only his wife. (00:31:50 - 00:37:50)
Plot hole: In the first film, Toulon fled to America and, when the Nazis found him, committed suicide in 1939. But this movie, effectively the prequel to the franchise, opens in 1941.