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 around 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 follows 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 work and the ships 'sink' inside the planet, were they are captured.
My Server runs on an middle-class VPS so maybe this has something to do with little processing power.