I strongly suspect there's something seriously broken when conquering an alien population by fire.
I have a pesky NPR who's been sending colony ships into my systems. He colonized some airless moons, so I sent a beam-destroyer to clean out his garrison. I fired one salvo of lasers at his ground troops and got a message that his colony had surrendered.
I went to the F2 screen expecting to see a colony on that world with an alien race inhabiting it. Instead I found a colony of humans! So unless you've put a zinger in that NPR can magically be generated with the same race as the player race, I assume there's a bug in the colony transfer code. Perhaps I should rename this race "Doppelganger", since they can obviously assume human form well enough to fool my sensors.
The next issue is that the colony already had a governor. And I didn't appoint him. When I went looking for him on the F4 screen he wasn't there, and someone else was "33rd Civ Admin". I assume that this is actually the alien governor, who never got relieved/captured and is still on the alien books but visible to me through his link to the colony.
I'll edit this message if I find any more weirdness.
[EDIT] - ok looks like the first issue might be Working As Intended. It turns out my bombardment killed off all the alien scum - I think I recall seeing that Aurora is set up to convert the population type to the conquerer in that case (hmmmm - but the status is still "Vanquished"). The second issue about the governor still holds.
John