Red John still being alive. The major problem I have with that is that one of two things happened. Jane knew from the beginning that it wasn't Red John and he killed, despite him making it clear that Red John was going to be the only human he ever killed. Or Jane found out after the fact which means he made a MAJOR mistake and is fallible and kinda takes away some of the magic from the character. They better do some serious explaining in the coming episodes or I will be disappointed in the show. Has been one of my favorite shows for a long time now.