Exiled from Continuity: Because of Hanna-Barbera claiming the rights to the Fantastic Four to create The Fantastic Four (1967), the FF weren't allowed to appear on this show. As a result, the episode "Doctor Doom's Day/The Doomed Allegiance/Tug of Death", which curiously had no problem using Doctor Doom, replaced the Four with the X-Men as his enemies, albeit referred to as the Allies for Peace.
Fake Nationality: The fact that this show was produced in Canada, and most of the comics starred Americans, created plenty of examples.
Keep Circulating the Tapes: Disney has owned TV and home video rights for even longer than they've owned Marvel Comics itself, but plans to release the shorts on DVD and Netflix became inexplicably delayed, bar some of the Hulk's shorts showing up on an out-of-print DVD of his 1990s cartoon. They also stand as some of the few Disney-owned Marvel cartoons unavailable on iTunes or Amazon Video. Averted in the UK and Canada, which have some official DVD sets.