Although not technically an Easter Egg (more like unused code), the Hot Coffee mod [1] to Grand Theft Auto San Andreas certainly cost the developer and publisher a lot of headaches and money. I can see why Easter Eggs would be forbidden after that experience.
I always found it absurd that in a game where the player character is a street criminal and most of the game objectives involve robbery or murder, a minigame depicting clothed dry-humping is what pearl-clutchers found to be a step too far.
[1]. https://en.wikipedia.org/wiki/Hot_Coffee_(minigame)