Hey, all,
I was playing as TEC. I had either made a cease-fire or alliegiance with another(were they Advent or Vasari?) faction(pretty sure they were allies, finally, though).
My intel wasn't up to date, So I jumped in, expecting to see them as I passed through. Their factories, extractors, research centers, etc, were all there; but the planet was neutral. Checking their diplomacy tab, I saw they were eliminated. I colonized the planet; but was unable to set up a new infrastructure there; Since they died freindly, I also was unable to target them with my ships to simply destroy them.
Anyway, just to bring it to your attention...Keep up the good work!!