When loading a saved game, sometimes enemy units become allied. I think this is because of the 'Change Faction Alliance' effect from the last patch. I think that loading the save file sometimes causes it not to work. I have heard that it can occur even without this command, however. Below is an output log and save file where this issue occurs.
Output log from someone who experienced this issue:
Save file (I think it is the first but I uploaded both just in case):
Customer support service by UserEcho