I noticed a few stacks of enemy units (they're pale blue in color, and I'm at war with them) on top of my city ('Bait').

http://dl.dropbox.com/u/5475789/EnemyUnitsOnMyCity.PNG

I was unable to attack them or move next to them (in part due to terrain adjacent to my city).

Deleting buildings 'underneath' the lowermost enemy stack (enough to also have an open area next to them -- without this open area next to enemy troops, when I moved in to attack my units attacked individually and not as an army, resulting in a windows crash as I've detailed previously) allowed me to attack that stack normally.

http://dl.dropbox.com/u/5475789/ModifiedCityToEnableAttack.PNG

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A similar situation a few turns later...

My city Crystal was captured (by a stack of 59 peasants!), pic after it was captured with enemy units on top:

http://dl.dropbox.com/u/5475789/EnemyTroopsOnCityCapturedFromMeBeforeIRecapture.PNG

The pale blue units were the capturing faction, the purplish units are another enemy faction.

I recaptured Crystal city, enemy units still on top:

http://dl.dropbox.com/u/5475789/RecapturedCityWithEnemyUnitsOnTop.PNG

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as aside -- stack of 56 units (from the 59 that took my city) defending said city:

http://dl.dropbox.com/u/5475789/56EnemyTroops.PNG