This is a fairly old issue.
I found an example of this when I was helping primal with his save game. I don't think I've had a game where this did not work on.
https://www.dropbox.com/s/0eap03qveygvr3y/P6-S170.EleSav
Situation: At the point of this save Primal's second army, lead by Vallisa, is out of moves right next to Delin.
1) Hit End Turn
OBSERVE: Delin will attack Primal's Vallisa's Army
2) Autoresolve battle.
3) Load the autosave.
OBSERVE: Delin is now right next to Vallisa's Army who now has all of their movement points. Delin is now sad because he doesn't get to eat Vallisa's army.
Expected outcome: Autosave should happen after all enemy units have completed their moves and resolved their combats.