Corrected entry: In the Season 4 episode "Mr Right", Timmy wishes that he was always right, and the magic makes it so that anything he says automatically becomes true. When he goes to tell Vicky he has fairy godparents, he actually says, "You'll probably be so busy that you won't listen to me," which Vicky refutes by telling Timmy that she's not only going to listen, but going to videotape him. But since he said that she wouldn't listen to him, the magic should have made that statement true and Vicky wouldn't have listened to him.
Corrected entry: In the episode where Timmy and Mark, the tentacled-alien from Yugopotamia, fight for Vicky, in what Mark calls "the Digifat", in the first round at the arena, Timmy wishes to be a robot, but turns out to be a pillow-shooter. But it has been specified more than once that Timmy can't wish to help him win a competition.
Corrected entry: In the episode "Power Pals", one of Timmy's superhero friends pulls out a small crystal and throws it into the cafeteria where everyone is eating. It lands in a drain near one of the tables at the back of the room and a giant table littered with diamonds called "The Table of Frienditude" appears. The question is, why would there be a drain out in the middle of a cafeteria?