I conquered an AI city. Then on the same turn I exited the city with my army and re-entered it. It said that I captured the city again, or so I thought. It turned out that I had actually captured two different cities. The other city was empty and I couldn't build anything, while the other one was the real city with all the improvements attached to it.

I am not sure if this is because I entered the city twice or because that AI actually had two cities on top of each other.

I will include the save file once I get back on the computer that has it.