I have a problem: If you maintain good relations to one of the minor factions or "flatter" them with influence, you get the message that you can heal your fleet(s) in their star system, upgrade them, etc.  But still, my fleet(s) are attacked every time i fly in there systems but not if i "drive" thought their system. Although I've never been hostile in any way.

Is this some kind of a (known) bug? Did i something wrong?

I have had this before as well but that was only with the war-like minor factions (the birdman soldiers (hissoto?), the agressive recycling robots(dueyans?), the underwater pig things,(Ghanast?) I simply can't remember the names well enough and dyslexia doesn't help with these naming schemes) so I thought it was just part of their base programming.