It only happened that once, and when it happened I didn't think much of it - so I don't have a prior save. No matter how hard I try I can't reproduce it.
I do have a save where the Sovereign gets XP every battle, even battles that she is not in, but not her entire stack.
https://docs.google.com/leaf?id=0B8p6Szpwj85oODI1ZGVkNzYtMGFkYi00OGZmLTg3YjgtOTVkYzlkMTk4ZTA3&hl=en&authkey=COG_zLoP
More Details regarding my first post:
There seems to be a bug where when an army stack is out of movement, but has a creature targeted for attack, and then that creature moves just right during the move phase the army stack attacks it before the end of the turn (before the research screen pops up). There also seems to be a bug where the army stack, having run out of movement and is targeting a creature, will attack that creature at the beginning of the turn, after the research screen pops up, but before I'm given control over the Empire again, and takes a huge chunk out of the armies subsequent turn movement.
I believe that my aforementioned bug occurred during the "free attack" that happens before the research screen comes up, and that's difficult to replicate because it requires the creature to move just right, and my game as it is either crashes every few loads or runs out of memory every few saves. From my first post, the second stack (no battle, xp) was out of movement, had just won a battle, was the top stack in the queue, and contained the Sovereign as the leader. The first stack (battle, no xp) was led by the Sovereign's daughter and had not been in any battles that turn.