I see. In that case I guess there's not really anything I can do besides restart the entire game and see if that works. I already went back & romanced bernard awhile back to get the bareshade upgrades as they were seemingly necessary to access a lot of the new content in some of the recent updates.
Maybe I'll rescue logan this time since I've always gone after bernard instead, if i do restart the game that is. But as far as i can tell, the werewolf plotline has no way to properly continue without rescuing Caleb first. Could be wrong on that i guess.