@Iris @joe I believe I figured out the cause. When a new player spawns in a system, any secondary populations that may have been on any planet in that system is removed. The planet displays that there is a secondary population on the planet until you explore the planet again, so if you check it before you put a fleet in orbit of that planet again, it will seem that there is still a secondary population.
The part about the colonise animation playing twice that I talked about earlier is likely irrelevant, I probably accidentally clicked the alert twice or something.
3 planets that I planned to colonise have been altered or taken by new players. 2 of which removed the secondary population (one Evolvanian one, the one I mentioned earlier in this thread, and the Skregon one shown in the video). 1 of which was taken by a new player.
This has wasted a lot of my colony ships’ time, and I think it would be better if the game prevented players from spawning in systems that have already been explored. Though I suppose that creates its own problems?
Video of a Skregon planet I was planning to colonise losing its secondary population because a new player had spawned in that system (can’t upload mp4 files here so it is a link): https://streamable.com/qfncj
Screenshots of a planet that I had previously scouted being taken over by a player when I returned to colonise it:
(The above planet originally had a different landmass and temperature too, but was altered as the new player was playing as Syntis)
I should also mention, I believe that all home planets should have an equal size and resources (or at least make it race specific, so ripchee has 80% beron and syntis has 70% beron to start with or something like that). Seems a bit unbalanced for some people like this to start with 20000km+ planets where as others (like me) start with home planets around 10000km in size and not all green densities.