Currently having this issue with the Nere fight in Grymforge.
Having the fight work correctly is already kind of a mess. Often, after blowing up the cave-in, Beldron will run through the fire and cause the Duergar to initiate combat with you (because I guess the fire area damage counts as you attacking him).
So when I finally got the Nere dialogue to initiate before combat, I saved on my turn so that I wouldn't have to go through that mess again. But after reloading that save and attacking a duergar, the deep gnomes react as if you had just attacked an innocent person and join the combat against you.
I don't know if this is the only combat where this is the case, but I haven't had another combat with this set of circumstances.