Plot hole: In the beginning, Rachel and Loomis are referring to Rachel's mother as being Jamie's step mother and Rachel refers Jamie as being her step sister. Rachel's mother is Jamie's foster mother and Jamie is Rachel's foster sister as said in Halloween 4.
Plot hole: Where exactly did all the other people go on the ship? In the beginning of the movie there were people everywhere then all of a sudden it's down to the main characters.
Plot hole: We discover that Teresa the maid has been turned into some kind of living zombie at the end of the movie. She confronts Alex and Megan near the end, and they run away from her and then fight with the Puppet Master. The issue of Teresa is then never addressed in the rest of the film, she just simply disappears from the plot and the scene. (01:13:35)
Plot hole: If the Devil made Claire blind again, how did she read the fine print of the devils contract with Toxie saying that there was an escape pod?
Plot hole: According to the detective at the end Walter believes Ray kidnapped his dog, assuming he saw the note that Ray put in Walter's mail slot. But if that note was grabbed along with Walter's mail and the wig it would have burned up along with everything else when the house exploded. So how did Walter know that Ray had his dog?
Plot hole: Given the store's being bought by a retail chain like Kroger's there's no reason Bill's partner can't sell him his share in it, get half the price they're receiving for it then have Bill make quarterly payments to him. They could've also got the new owners to keep Bill on as manager as well as keep their employees or void the sale.
Plot hole: When the teens in this film come to camp, they see in the bathroom a sign spray-painted by one of the kids from Part 2 that says "Fuck Angela Baker." This doesn't make sense because in the second film everyone only knew her as Angela Johnson. So the sign should have said "Fuck Angela Johnson."