I try to place cities where they will have the best growth prospects; if there are a few odd tiles uncovered, I don't generally worry about it. If there are a number of them in an area, I might make a city to use them. I usually try to avoid overlap, but I don't go out of my way to do so, and just about anything will override this tendency.
If you are not in a democracy this can backfire big time. The AI can send in a diplomat to bribe the city out from under you, especially if it is small (as I would expect a city used for that purpose to be). A fortress with a few units should be sufficient in most cases to deal with enemies (unless they are using lots of bombers against your troops, as fortresses don't give bonuses against air units).
Or you might build a city on a mountain, to close off a pass to an enemy- because it will mean an impregnable fortress once walls are built.
If you are not in a democracy this can backfire big time. The AI can send in a diplomat to bribe the city out from under you, especially if it is small (as I would expect a city used for that purpose to be). A fortress with a few units should be sufficient in most cases to deal with enemies (unless they are using lots of bombers against your troops, as fortresses don't give bonuses against air units).