I don't know if this is related, but anyway...
Twice when fighting robot guardians I've ended up with a second, conquered (empty) colony on the same planet. In both cases, I had not ordered my units to cease fire after destroying the last enemy, and the conquered colony appeared after the next interval. This has never happened if I cease fire. I've never tried to deliberately duplicate the problem, however, so I'm not sure about the cause. Using 5.20, not 5.30.