I pick up the werewolf totem but it doesn't change the status of the quest at all and Aela is nowhere to be found. So I can't do anymore quests for the Companions, and nor can I ask someone to follow me anymore becauuse they just say "looks like you already have someone."

I am now bugged out of the main quest, the companions, the civil war, and cannot have a follower. Awesome stuff, at least they have a patch to fix the 8000 quest bugs!! Oh wait...