When I use the benevolent ideology trait or the mercenary ship to flip planets, I can 'trap' the garrisoned fleets on top of the planet icon forever. This has no serious gameplay consequence, apart from the enemy losing control of the ships (it doesn't prevent me for garrisoning the planet). It is only slightly annoying really, when I click the planet to bring up the planet management screen I get the fleet screen instead.
I do not think this happens when you culture flip though.
Anyone else notice this bug?