This has been a problem for quite a while.  (Was actually in WOM as well.)  The stacking rules seem to sometimes allow multiple stacks to enter the same space.  I just faced an AI army of 5-6 stacks of 7 or 8 armies each all moving together in the same space.  (Actually it was kind of fun, as I had some mana saved up, and just fought 6 blast the huge enemy army with a single fireball battles in a row.  The AI's power level dropped by about a hundred points.)

I'm not sure what the conditions are under which it happens, but it's always disconcerting.  If it would be helpful, I can check to see if one of the autosaves still has that stack of stacks in it, but it doesn't seem to be that hard to reproduce.