I've noticed a few bugs in my playthroughs, but these are the two I remember right now. I'll post more as I re-encounter or remember more.
1. In the archive, past runs save twice for some reason. I've played through the game twice, and each are logged in the archive twice, so it claims I have 4 past ships.
2. During the settling decisions, if you send the colony ship back to Earth with AI, the text reads something like "the ship will take well over six centuries to return to Earth," which doesn't make sense, because it only took me ~80 years to reach that planet. Surely an AI-driven ship with no human payload could make it back to Earth in at least the same amount of time.