I attacked a Kraxis city that had eight units, the majority of them were wounded champions. Only three of the nine showed up in battle. After they were defeated, I gained control of the city, but the rest of the enemy units remained in my new city.
I tried reloading several times and consistently got the same result.
Originally, this happened using frogboy's 1.19 beta version. However, I switched back to 1.1, reloaded from the original 1.1 save file, and got the same result.
You should be able to duplicate this error by opening the file BuggedSave and attack the nearby city with Othollo's army. The file BuggedSave2 shows the aftermath.
Does anyone have a workaround for this error? It seems as if this game is over.
EDIT: Fixed typo and minor detail.