Context: one of my cities (blue faction) had been conquered by the red army. I took it back but, even after many turns and a save/load, two cities seems superposed with 2 different names. The red one even had faction-territory borders during a few turns. And I can click either on the blue city or the red one to select it. 

After the first screenshot, I sent my 2 wolves to kill the red unit. The red shield stood still. Then I sent them back to the city and the game said "You conquered city of XYZ" (even though it was already mine) but names are still superposed.

Strange: I can still select either of the 2 cities. (And why is there 2 by the way?). But only Alaana can build or traîn anything.

