Hi, I've popped the bulk of your post in spoiler tags. Feel free to extract some non-spoilery context to let people know where your issue is.
As far as I'm aware, in the scenario you outlined, Halsin should still be
in the separate Worg Pens room until you tell him the leaders are dead.
If you haven't already and another user here isn't able to shed light, it might be worth submitting your savegame to Larian via the "Report a Bug" option on the game launcher, if you haven't already.