I see this with games involving multiple foes and capital kill. When you take the capital then all occupied cities stay as they were and all units (land, sea and air), all stop in their final location. Annoyingly armed satellites also stay active and will take pot shots at you. The last is, I think, fair enough but I do think all other units should go to their nearest city and disband. Then again, some enemy units may not have got the memo and if you encounter them while in transit then they might choose to engage in combat. Perhaps a random setting, some surrender, some don't?