I noticed this within the last couple of days that occasionally NPC's will attack their own allies both on ground and space (and no I'm not using scramble sensors which wouldn't affect ground anyway). So far I've witnessed this with the Gorn during the Researcher Rescue mission, the Breen ships in the daily missions and the Mirror Universe ships in the story arc.
While being amused by this, it made things considerably easier which I'm not sure we want that
Just an update to this. While I haven't noticed it as much overall, last night I was running one of the missions where you need to clear the mines around stranded freighters and got a laugh as the mines went active and blew themselves up because they were "attacking" each other.