Something similar but even weirder: AI1 conquers AI2's only city, but (maybe because there were more than 9 units inside) AI1 sovereign remains standing on top of city (not inside). When I conquer this city shortly after (by clicking on a building, center square talks to AI2), AI2 sovereign does not budge.

Here is another example of that: Kraxis troops and monsters in the same tile.

Here is the savegame: http://dl.dropbox.com/u/10090435/kraxis-monster%20sharing%20tile.EleSav

If you move an army immediately it was possible for a human player's army to exist on the same tile as a monster.  Though that was a few patches ago.  But I think it is still possible with regards to the sequencing of players - human players can go when they like, and if you are really quick it can get messed up.

I mean for the human players.  Human players can only get stuck on the same square as AI monsters if they execute a move order immediately when the turn starts.