This happened to me once. I had just run into Freeport V and blown up, attempting to pick up drifting cargo that was very close to the planet. I had just saved the game, so I reloaded. Lo and behold, the planet was invisible. I noticed two more cargo crates were INSIDE where the planet should be. After saving again and reloading, the planet reappeared. I carefully picked up the first cargo crate and departed, still able to hear the 'beep' signals from inside the planet.
