I just vaporized some minor faction (which was...interesting...as I killed a 34 HP wolf unit with one spell...somehow...) but when I got back to the map (after leveling my Queen and embued champion). The city and the sovereign's stack disappeared!
I took a screenshot. The village was right next to that Ogre Camp in the screen shot. I got 2 crystal from somewhere.
BTW: This is a faction I created from xml outside the game, in case that matters. If wanted, I can put up the XML file that defines it.
Debug.err is attached.