I don't know that Pegg deslikes anything.
Oh, that is not accurate. Just Google Pegg and Episode 1: The Phantom Menace and you'll realize that the Star Wars prequels are high on the list of things he actively dislikes.
As for ID, part of the creative process, even when you are a part of the creative work, is always a minor disagreement over choices or what you would prefer to do versus the writer or director.
Also, part of film making is second guessing yourself as to whether or not you made the right choice. George Lucas once made the observation that great movies are never completed only abandoned. While many may not agree with GL's approach there is definitely a dissatisfaction with the creative work. So, its not something new.