"The Ricardos Visit Cuba" - I Love Lucy
This episode isn't necessarily inappropriate or controversial, but there came a point where it didn't feel like it should be aired (apparently.) In the episode, Lucy, Ricky, and Little Ricky went to Cuba to visit Ricky's, Uncle Alberto. They wanted to get on his good side since he wasn't happy with the fact that Ricky married Lucy and not a Cuban woman. After the US went south with Cuba in the early '60s, the episode was pulled.
"Boston" - Aqua Teen Hunger Force
Aqua Teen Hunger Force is a bit of a weird show, that's for sure. They ended up making an episode that was a parody of a marketing issue that the ATHF team faced. In the marketing for the film, the team made claims that homemade Lite-Brites were actually bombs. Unfortunately, the Boston police thought that it was true, and the entire situation ended up costing $2 million in fines and fees. The parody episode was taken off the air once a terrorist used a homemade bomb in Boston years later.