Supposedly the wolf has no recollection of his human life and takes whoever happens to be there as his victim. The fact that he would run away upon seeing his sister is quite strange.
I know that Liz is in a state of shock over the wolf encounter, but since Julia had just told her about Amy's disappearance, it's hard to believe that she didn't connect the two - especially when Amy told her her name (I think Julia had mentioned the name).
When the show started, apparently David and his father had only recently moved back to Collinwood. Presumably he had a more normal life before that. But, when he told Amy that he was surprised that she wasn't afraid of the storm, that most girls would be, I was wondering how he'd know anything about it. It wouldn't seem that he knew any girls, or any other boys, either.
Chris' living quarters - it looked like the same room in the inn that we saw him take the last time. What happened to the clerk? Wasn't there any police investigation? Given the state of his room, wouldn't he be under suspicion? He's still living there as though nothing had happened!
How does Julia do it? All along it would seem that she has moved into Collinwood and spends almost all her time with Barnabas or doing things connected with him (the whole experiment business, etc.). But, from her interactions with Amy, it would seem that she isn't just the head of Windcliff and giving instructions from afar, but has apparently been continuing her regular work. She used to have to be up all night with Barnabas - how could she work without any sleep? But now, Barnabas is "normal" - yet the things they do still seem to be mostly at night.