GalCiv3 Forums
When you flip a planet any ships that were around it need to be removed/ejected from the planets space. Otherwise they seem to sit there and you can't move in and place any of your own ships.
I have often experienced this as well. The flipped faction's ships seeem to forget they belong to the faction which owns them, they remain docked at the planet, and will not allow one's own ships to dock.
Perhaps this was thought of as a "feature" at one point, but it looks like a bug.
This is as old as the game itself. This is either WAD and an odd decision or so low-priority that it will never be fixed.
Ran into this as a side issue- tried to move a colony ship there to pick up excess pop and accidentally started a war with the race that I had just successfully flipped a planet from- just because their ships hadn't left.
I'd throw my input into having this addressed one way or another.
Thanks for the report. I've asked the team to fix it.
I had this happen in my game today. I submitted the autosaves, another save and some information on Ticket ID #USJ-534-22868. One of the saves is one turn before it happens, so maybe the team won't have to look far to find the problem.
The ships should be flipped along with the planet should be an easy fix. 
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