Revealing mistake: Whenever Will does one of his fancy jumps (which make him actually appear more like a monkey than a wolf) you can easily tell that he gets pulled up by a rope because always accelerates on the way up. If he were jumping his maximum speed would be at the moment when he takes off. The softened landings enhance the unrealistic impression. (01:06:35)
Revealing mistake: When Stewart jumps against the iron bars in the final bite-out they bend like plastic. (01:48:10)
Revealing mistake: After Will bites the deer there's a shot of some birds taking off in front of a rather crudely painted night sky backdrop. (00:49:30)
Answer: It was Stewart. The wolf, as Dr Alezais says, removes everything from a person except for the person's nature and heart. Stewart, when talking to Laura at the estate, states that she knows what happened to Charlotte, which was his subtle way of saying he had murdered her.