The exact same thing happened to me yesterday. I was playing a game as Kraxis, and I had unlocked all 9 spots in my army. When I entered a battle my sovereign was stuck in the bottom left corner of the battlefield. He was unable to move or attack, but he could cast spells. This happened two times in a row on the same battlefield, and I would venture to guess that it has something to do with there not being enough available spots for the sovereign to spawn on.
You can see the green square around Karavox on this screenshot:
