I ran into a bit of a difficult situation: I decided that in the full moon arc I will help normal Logan instead of Bernard. I also went to the witch to get the quest where she wants the alpha male fang. I go to the wolf den dungeon and encounter werebernard, whom I capture and put in my jail. So far so good, but now, I can't really do anything, if I want to go deeper into the dungeon to find the alpha male, the game says I am not prepared or something, and if I free Bernard, nothing happens, so I am afraid to do that and mess up something, I went back to a save where he is still in my jail ( I also can't even use Wolf's bane on Bernard either). Can anyone help me, or just have any information regarding this issue? :/
You should be ok. The alpha wolf is not behind the door in the bottom right corner of the wolves den, it is in the upper right hand corner, marked by an exclamation point (!). You don't use wolf's bane to treat Bernard, you need antilycan. Go get the alpha wolf's fang and you will be able to continue the Full Moon event.
To lure the alpha werewolf out you need to fight 2 werewolfs and he'll appear on the bottom right with an "!" Marking him, doesn't matter if you win the fight with the 2 normal werewolf by teasing or attacking, doesn't matter if you surrender as well, you just need to have those 2 fights to lure the alpha werewolf.
Did you go back to the witch at night and end the task for antilycan? Are you checking the wolves den at night? Check the events log, Bernard's part, see what it says. It takes a couple few days for him to show up. I started over and don't got any saves, but I know there was a task in the event log to go check the cottage in the forest at some point and I remember it showing how many days til Bernard would appear in the den. The events log is pretty specific for the Full Moon event.