Girl Trouble / School Dance - S3-E18
Continuity mistake: Besides the fact that when Helga is sharpening her pencil, the desk arrangement changes, one of the students visible when she looks at Arnold is...Helga.
Darkness and Light: Part 1 - S1-E11
Plot hole: When Hulk and Banner have been physically separated by the nutrient bath, they are both wearing tattered pants. Given that Hulk and Banner were previously occupying the same body, this should not be possible. Hulk was the one that went into the nutrient bath, so if Banner's body was separated from Hulk, then Banner should be naked.
Suggested correction: It was done deliberately as a form of censorship. They didn't want to show Bruce's genitals.
Explaining why the mistake occurred doesn't invalidate it. Unless you're suggesting the nutrient bath also was able to duplicate the pants.
You realise a character can be drawn naked without actually showing their genitals (and/or breasts in the case of women), right? The Little Mermaid is a good example of this.
Deep Metal - S3-E2
Continuity mistake: Depth Charge fights Rampage on the beach. Throughout the whole episode, Depth Charge has four fingers. But in a shot when DC doubles over in pain to clutch his wounds, he has five fingers.
'Unmei no sentaku' mitaina - S1-E6
Plot hole: Akito's attack is point blank, on a ship part of a fleet with Distortion Field activated (basically, they have shields, like the good guys' robots). The explosion he causes is according to Ruri's damage report big enough that it managed to vaporize 80% of the ships they were facing, but his Aestivalis and the other 3 right floating nearby make out of it literally without a scratch. (00:05:10)
Monkey Fun - S2-E13
Other mistake: Season 2 episode 13 "Monkey Fun": Just before the enlarged Titano appears at the zoo, there is a family watching normal-sized monkeys in a cage. The family father (farthest on the right) has a drawing disorder with his eyes: their pupils look up and down, respectively, giving him a rather goofy expression.
Continuity mistake: When Steve sings the Blue's Clues theme, he is wearing tan shoes he wore in few other episodes. When he drops his notebook after the theme, he is back in his brown shoes.