He dislikes how all of his projects have been filmed so far (in general, he doesn't believe in film adaptation, saying that they were written for one medium and so should stay there), and there have been some other complications (such as a lawsuit accusing him of ripping off another screenplay when writing League of Extraordinary Gentlemen
He also has issues with filming things that he doesn't own, such as Watchmen
, where DC played fast and loose with the contract rules on certain merchandising items and on ownership in general.
From what I have heard he is disgusted with the Hollywood system in general and very protective of his work-I don't think he wants them to change one word. Literally. I read V and saw the movie and it was darn faithful-but he disowned it.
It was a good film on its own, but it completely changed the message of the original (and he also disliked the way the British characters were written, which he thought was laughably inauthentic).