SW3, Bug

Uh, that sector is "owned" by merc faction. By farming them, you've flagged them as hostile.

Edit:
The problem stems from hired mercs sharing same faction as "mercenary faction", that's my best guess. Solution, don't hire mercs until you've met a rep-fixer who can fix your problem with mercs.

Edit 2:
This is similar to the berserk hack bug to un-hostile them, and then suddenly having your other allies hostile you.