I can confirm this from one of my solo games as well: a pirate raid engaged me near a planet, and two of them got close to the planet surface. I exited the game with them there, and when I started the game up again they both spawned inside the planet. They have been stuck there since. Restarting the game or changing sectors does not have any effect.

Possibly also related: Deleting a weapon effect computer block and restoring it with undo will restore all its logic connections to the effect modules, but does not reconnect it to the tertiary weapon slot it was connected in.