Allies attacking me

I'm doing a terran playthrough. I am very late game and have a shipyard in getsu fune which is supplied by a material factory in asteroid belt. The terran patrols in asteroid belt killed about 50 of my miners and started attacking my station. My reputation dropped from 30 to 28. When I go into the sector I see the terran patrols as red and hostile. I pulled out all of my ships and set global orders to show asteroid belt.

This obviously makes my station useless which leads to big problems at my shipyard. I also am cut off from the majority of terran space now since asteroid belt is a major middle sector to travel through.

What I think happened is one of my ships must have hit a terran patrol ship by accident and triggered the whole thing.

Kha AK had been attacking my miners in asteroid belt, so I sent in 20 takos, 8 katana, an Osaka and an asgard to defend my miners. The asgard was to find and destroy the khaak base, which I never found.

I may have had a flack turret on the katana as anti fighters. They may have damaged some local patrols.

My question is, how do I get the local patrols to stop being hostile? How do I avoid this from happening again?