Plot hole: Goldie Hawn's character obviously has lost a large piece of her spine when being shot, as seen through the hole in her body. So how does she keep her upper body up straight? When Meryl Streeps character broke her neck she couldn't keep her head up, so why can Hawn walk around as normal?
Plot hole: At the end of the movie, when Lonette comes across Frank's dead body, she asks Nails what happened. Nails tells Lonette that he was pushed off a building by Holly Wood. Lonette then asks if Holly was in doodle form when she killed Frank. Nail says she was. There would be no way for Nails to know either of these things as he was trapped in the fountain pen when Frank died and wasn't released until the Spike Of Power was removed.
Plot hole: At the climax of the movie, the bully reveals Link to be a caveman by among other things, breaking into the High School and stealing his student registration papers, containing among other refuse, the vaccination license of a dog. Problem is, wouldn't the school staff have already checked those at the start of Link's time as a student?