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. This happens because the shot is taken from the episode "Helga's Love Potion."
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.
Plot hole: Didn't Dexter ever notice the giant fire pit in the ant farm?
Suggested correction: This is more of a question than a mistake. (To be fair, I don't think questions were a feature yet back when this was posted.) No, he didn't. He only noticed the fire pit (and the colosseum) when he was inside the ant farm. It most likely just wasn't visible to him from the outside, or it was too small for him to see it.
Continuity mistake: The package Steve received from Mailbox is briefly visible before Mailbox comes in. You can also see a crew member's hand holding the package as Steve grabs it.
Deliberate mistake: Season 2, episode 6 "Identity Crisis": When Bizarro starts decaying into the parody form of Superman, his costume goes with it; the blue fades, and even the 'S' insignia changes. Strange that superhero garments change right alongside their wearers when they suffer from an unstable genetic effect. Were the clothes cloned right onto his body, instead of sewn?
'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)