So I decided to play humans for once, and had just saved a splinter ashdar colony from the pirates (who of course didn't join me, because I was humans). I went and built an outpost on another planet in the system, hoping that'd stop the Ashdar Imperials from bombing their brethren. (Don't remember if that worked.) Then I started research on hyperspace anomalies, causing the Herald to visit me in that system. Traded with them as normal, but a bit afterwards realized I couldn't contact the independant colony. The star name was a unique shade of grey, and eventually when I tried bringing up the bombardment menu noticed that the colony said it belonged to the Arda Seed.

Probably not intended?

Curious. Could you upload that game so we can take a look at it?

(with the game in question loaded, in Options menu, click "Upload Game Logs")

Uploaded it, it's game_9021. Also undid a bunch of turns to get a pic of it. (But submitted the log from the end of the game.)