i started a new game because i still kept getting the message. and got the message again. after some testing, i figured out that you can go through the hatch to the werewolf BEFORE the captain unlocks it. If i waited till after he unlocked it to go though, i didn't get the message.
might want to see if you can disable the hatch until after the captain unlocks it.
ok. i started a fresh game and yes it's locked. I think it might be more like this: if after the captain unlocks the hatch, you save and exit. when i'd load back in, i'd have to not only bring up the quests, but also talk to the captain to have him "re unlock" the hatch (although it was already unlocked) to not receive the error after killing the werewolf.