Yes... there was one character who would turn my conjured atronach against me several times. I just couldnt work it out.... so i killed him.
I dont think it is a glitch, seems like some cool spell or however they are doing it .
Have only had one character do it.
There is an expert conjuration spell called 'Command Daedra' that allows you to take control of summons up to level 20.
If its the same spell, storm atonachs and Dremora lords should be immune.
It may be a more powerful version that even controls them as well though.
Maybe try dead thralls if that is the case?