There are plenty of stories of authors being upset over how adaptations of their books turn out. Some of the time, the adaptation is actually good, but the author still finds fault with it for one reason or another.
*PL Travers disliked Disney's Mary Poppins film. The film Saving Mr. Banks (about Walt Disney working with Travers to adapt the book) downplayed Travers' hostility toward Disney.
*Stephen King initially hated Kubrick's The Shining, though he seems to find it tolerable in recent years, as he allowed his book Doctor Sleep to be adapted as a sequel to the Kubrick's The Shining.
*Roald Dahl hated Willy Wonka & The Chocolate Factory, to the point he prevented any attempts to make a film based on the book sequel The Great Glass Elevator.
Going back to Moore, it seems the only adaptation of his work that he is OK with (as in he has not publicly expressed disapproval) is the Justice League Unlimited episode that is based on "For The Man Who Has Everything".