So In this save game, I just conquered a city belonging to Tarth called Barmen.  For some reason, though, the computer also has Imperium on top of that city, which belongs to Magnar.

I've uploaded the save game file, so you can take a look at the bug yourselves.  I can't access the Gilden army that's inside it, but I can bring up the build queue of Imperium (which belongs to Magnar, not me).

https://docs.google.com/open?id=0B6fIfd2B6EnEMWNjNzcxMzgtMjNmMy00MDRhLTg5NTctOWM0OWNmNmE0ZTA0

I tried declaring war of Magnar to see if that would do anything... it didn't.