I'm leaning towards the bug interpretation for why the world was like that. I don't have those game files around anymore, let alone a before and after, so submitting it would be tough.
I know that the aliens had a colony cost and a negative growth rate. When I planted some spies, and later some soldiers, I had a human colony on the world. After conquest, I flipped back and forth between the humans and the aliens. Both had colony costs. Alien colony cost was 2.0, typical of a bad O2 percentage. (The humans did not have a negative growth rate because no human population was present and I can't recall their colony cost. I think it was 2.0, but am not certain.)