I have done that event (killed the alpha as Logan) and unlocked the Misty Abyss not long ago. How to trigger the Troubles in the Den event?
Edit: I have also encounter Logan visiting my new house in Bareshade.
I haven't started on the new content yet because I started from the beinning again.. I think you should visit Logan and talk about the rumors?
I just figured it out (I didn't notice that it started when i talked to Logan, I was skipping the dialogue because I as speed running). You just have to follow those exclamation marks around the Wolf Den lvl 2 and Misty Abyss.