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?
Character mistake: In the third instance where Superman manages to get rid of Mxyzptlk, he uses an article full of typos which spell the latter's name backwards as KLTPZYXM. Among the incorrect words is the word "citrimes", in which Superman has included an I and a T, so the correct word in context with the rest of the text should read "crimes" and thus the errors would spell KL-I-TPZYXM. Since there are no vowels in MXYZPTLK, however, what is the additional I doing here - and why didn't Mxyzptlk bother to mark it as a mistake, either?
Double Dose - S2-E10
Factual error: Season 2 episode 10 "Double Dose": When Superman snatches Parasite's escape boat and hauls it back to Stryker's, Parasite attempts to blast him with a shotgun found aboard. But somehow the animators appeared unable to decide whether the gun should be a double-barrel or a pump-action type; and building a double-barrel pump gun would be impractical due to additional weight and bulk.
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.
Heavy Metal - S2-E23
Continuity mistake: Season 2 episode 23 "Heavy Metal": In the beginning, when Metallo and the Intergang goons raid the bank, the goons use conventional sub machine guns. But when they start tearing through Irons' neighborhood looking for Superman, the goons use the same guns, which have, however, suddenly become laser blasters.
