It's happened to me, it can happen to you.
This is a B_U_G. It happened to me once in a city that was undefended, and that the AI had clearly targeted. I was going to reinfoce the city with some mech inf., but when it got there, it was killed entering the city!
The Colors indicated the city was still mine, but I was thinking it might have been a graphical error, and that the enemy AI had captured it. It was difficult to tell if it was still under my control since when I right-clicked, sometimes it would say "take me to your leader" - which would take me to the AI that was comming for me, the Persians - , and sometimes it would show the city screen.

So much for a graphical error.
No amount of bombing, attacking, fighting would allow me to retake the city.
Reloading your autosave turn will fix the problem.
Oh yeah, and for what it's worth, I too had just nuked the french (Note: This is not the civ that appeared to "control" the city some of the time). So this problem is obviously linked to nuclear weapons use. And maybe, dare I say it, a bug linked to the french (you never know).