I've mentioned this somewhere else in these forums, in the general forum I think, but I'll repeat it again. NEVER use the delete key in the cheat menu to destroy cities or forts. Use other methods, like having enemy units walk on size 1 cities. If you use the delete key, sometimes the info of which city is using the tiles isn't deleted, and a ghost city continues to use them after its dead. I've never had the problem about multiple cities in one spot, but its probably related to the same thing.
Generally speaking, be extremely wary about where you place a city- don't place it somewhere and then think, nah, I'll place it one square over. If you do that kind of thing, save often and backup your saves.
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