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.

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.

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.