Assuming you mean the female assassins and the male assassins are fighting each other, the reason is the faction set-up - the Black Ops fighting the standard Grunts was something that didn't get introduced until Op4, so Valve just set the female assassins to be the same faction as the hgrunts - Human Military. Op4's male assassins use their own faction that's hostile to Human Military, IIRC. I seem to recall they also changed the female assassins to that same faction in Op4 as well, which is what I would recommend doing.
If that's not the issue, it's probably still an issue with the factions, so double-check those.