After a lot of colony frustration due to mods I decided to try a complete vanilla version.

Everything went fine until the first Hegemony inspection fleet came. 3 Patrol HQs werent enough to kill it, so I clicked on it and to my surprise it said that this fleet was acting without its goverment approval and hence attacking it would not cause me problems. Ok, so I wiped it out and promptly got the -5 relations with the Hegemony anyway.

Is this a bug or am I misunderstanding something here?

As to what I trying to do: Im trying to get the isolationist and explorer gamestyle to work, I even tailored my colonies to be mostly self reliant and export as little as possible to the market. Yet it really seems the game doesnt want to let me.

What I see happening is that the game will force me to constantly run "between defend my colony", followed by "mission to recover favor with that faction that just attacked me", then back to "defend my colony" again.

This kinda eliminates the trading and exploration gamestyles once you have a colony.

It really feels like there is a lack of diplomatic options for the colony and factions part. Factions that like you or have alliances with you really shouldnt attack you or you should be able to pay them off.