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.