Accidentally posted this under the wrong account first, but I will delete that post. 

If you attack a city that is not under siege and there is an army nearby the game treats the battle as if you attacked the army, not the city. 

Save file attached.  If you attack the city (pick any tile the army isn't standing on) with one army, the minitor will retreat from battle. Attack again with the other army and you win the battle, but don't get the city. 

Vaulters - City Attack.sav

I just had a few minutes to check your save file, but I could not reproduce the issue. I'll need more detailed repro intructions.

When I saved the game, the minitor was standing on a city tile. However, as soon as I loaded the save file the army moved off the tile.

The bug happens most often when an army is standing on one of the city tiles. Can you use the Dev console to add a army and have it stand on a city tile and try again.