With Beta 4, I had the following problem:
There's a enemy planet with ships in orbit. When the planet switches sides to me (culture flip), that ship remains in orbit - still belonging to the other faction. It remains there, I can't attack it, but it's still shown in orbit, I can even try to upgrade it, showing me the upgrade window with the factions ship types but all disabled.
Where as when one of my colonies flipped to the other side, all my ships in orbit changed sides too and I have to fight them...