If the multiplayer Server is restarted or was inactive for some time and a player joins again, sometimes all ships that were parked on the planet or near the planet end up inside it.
It happend areound 6 times to me now, a fleet that was idling neear a planet and 2 small ships that were on the planet were caught inside it, the only way to get them out is add them to a fleet that flows thew player and fly away until the sector with the planet is unloaded. Otherwise the ships just keep flying against the inner boundaries of the planet.
I think that the planet is loaded after the ships, so the collison detection does not worl and the ships 'sink' inside tha planet, were they are captured.
My Server runs on an middle-class VPS so maybe this has something to do with litle processing power.