Plot hole: The children decided that they hated the Powerpuff girls in one day. Then how did they have supervillain costumes and a van? The mom said they had lots of time to prepare.
Plot hole: I don't think the police would throw the wife and children in the same jail cell as Harold.
Plot hole: Buttercup knocks out villains' teeth so she can get money from the tooth fairy. This makes no sense whether you believe in the tooth fairy, or not. If you do believe, the tooth fairy only gives you money for your own teeth, and I'm sure would be able to tell whether they're your own teeth or not. If you don't believe, and think it's the parents giving the kids money, then it's the professor who's giving Buttercup the money. You'd think he'd be suspicious about where Buttercup is getting all those teeth, and would question her accordingly.