The tree ornament that Will's father hangs on the tree is not the same ornament that Will picked out and handed to him.
A red gasoline can is labeled "gazoline", which is only the correct spelling in Haitian Creole.
In the haunted school story the characters claim all the windows have bars and thus they can't escape. When the character later uses the restroom there is a large window with no bars.
In the storage room, Ben identifies some figures as a nativity scene that wasn't put on display. Molly comments "They can't open display a nativity scene anymore. It's the war on Christmas.". St. Joseph's Academy is clearly a private religious school. Private schools can put up nativity scenes and still do.