"201" - South Park
Yes, South Park has always been problematic, but never so much so that an episode was wiped off the grid... except for this one. Episode "201" is a notorious two-part episode that depicted the prophet Mohammed along with other religious figures. In religion, depicting Mohammed in any way is considered blasphemous. This episode sparked rage in a lot of folks. The animators tried hiding the figure in the second part (pictured) but they only made it worse.
"Dial M For Monkey: Barbequor" - Dexter's Laboratory
Dexter's Laboratory was a total winner for Cartoon Network. Kids and (most) parents loved it despite its bizarre humor. The episode "Dial M for Monkey: Barbequor" featured the popular Justice Friends. One villain, introduced as Silver Spoon, was introduced. He was a parody off of another superhero, but fans of the show weren't happy about how Silver Spoon was portrayed. The writers completely holed him into a gay stereotype and fans felt that it was unfair to the gay community. The show was ripped from all platforms.