I suspected that a while ago when I ran into a few hostiles from the Desperate citizens clan and my companions from the same clan just stood there and did nothing while I was getting beaten up. Now I did some testing in debug and my guess turned out to be correct. NPCs from the same clan will never attack each other, even if some of them are your companions and some of them are hostiles attacking you. Companions fight hostile NPCs from other clans just fine but don't touch the ones from their own.

It would be great if this got fixed because right now apparently you can't have the same clan spawning both friendly and hostile NPCs withouth above mentioned scenarios, so you have to set certain clans to friendly only (default setting of the first clan).