Father Time! / Apartnership! - S1-E4
Plot hole: Timmy uses his heat vision, that he previously wished for, to win the race for his future dad. But it's revealed later in "Smarty Pants" that if you use a previous wish in a contest, it is magically taken away because it's cheating.
Suggested correction: That is true, that rule was mentioned in a later episode. However in the episode Christmas Every Day, it was revealed that new rules could be added at anytime. So it's possible that the rule simply didn't exist yet. Although, this plot hole may apply to any episode released after "Smarty Pants."
Plot hole: Season 6, Episode 5 (overall episode 73) "The Good Ol' Days / Future Lost": In the episode "Future Lost", when Mark is hugged by several students at school, wouldn't he possibly freak out, since he is a Yugopotamian who doesn't like being hugged?
Plot hole: In "Oh Brother!" Timmy wishes for a brother who will beat up Francis and some other things. How come he doesn't beat up Francis, even though Timmy wished for it?
Suggested correction: Remember that episode where Timmy tried to wish something bad would happen to chip skylark? Da Rulez say that you can't wish that someone could be injured/beaten/dead.
Fairy Fairy Quite Contrary / Nectar of the Odds - S2-E10
Plot hole: During the magical duel, Jorgen counts off the seconds until the end; '3,2....' Remy then screams at his godparent, and about five more seconds pass. Time should have run out.