Continuity mistake: Even though the moon plays a leading role in the movie its phases get mixed up in a big way: Before Will has his first night out as a semi-wolf there's a shot of a half moon. That's not only just a few days after the full moon when he was bitten, but it's waxing to boot. In the next night, after Will calls Laura, apologizes for his vanishing, and asks her out for dinner there is another shot of a slightly fuller moon, but now it's waning. However, two days later near the end, when Will is locked up in the barn, the moon is full again. (00:46:40 - 01:05:05)
Continuity mistake: In the beginning of the film when Jack Nicholson hits the wolf, his car spins around 180 degrees in the snow, but there are no marks from the wheels in the snow when he approaches the hit wolf. (00:03:25)
Continuity mistake: The black deer Will digs his teeth into is not the same light brown one he was chasing. (00:49:20)
Continuity mistake: The scratches appear in Will's face before Stewart touches him with the pitchfork. In the next shot they disappear, to be back in the shot after. (01:49:20)
Continuity mistake: When Laura tucks Will in the two top buttons of his shirt are open, but when he jumps through the window a little later only one. (00:47:30)
Continuity mistake: When Will drives along before he hits the wolf there are deep tracks in the snow down to the asphalt. When he walks over to the wolf after he's hit him the snow is almost virgin. (00:03:25)
Continuity mistake: Jack the "half-wolf" attacks a deer in the woods and bites its neck. But when he raises his head there's not one drop of blood anywhere (in his teeth, mouth etc). (00:49:40)
Continuity mistake: When Will and Laura enter her place after he has made her fall from her horse her jacket gets half unbuttoned between shots. (00:38:00)
Continuity mistake: At the Alden party Will's tie knot is different in every scene: When he eats, when he walks in the garden with Alden, when he meets Laura, after he stumbles and holds on to Laura's breast, and when he gets back inside. (00:12:15)
Continuity mistake: When Will talks to Maude in his office his glasses vanish from his nose from one shot to the next. (00:08:05)
Continuity mistake: When Stewart talks to Will and Maude in his office about her obligations to MacLeish he is standing behind his desk with his fingertips on the table. When the camera angle changes his hands are on his hips. (00:09:10)
Continuity mistake: When Laura and Will sit at the lakeside and he tells her about his experience after being bitten by the wolf the choppy lake turns calm between shots. The light changes as well from dusk to daylight. (00:43:45)
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.