Docked entities disappear from a ship when moving from an unloaded sector to a loaded one.
Sometimes they leave behind a "hitbox" so collisions will take place where the missing item should be, other times the entity is simply gone.
Sometimes reloading the sector returns the missing entities, sometimes they simply disappear, other times the formerly docked entity is found floating in space.
I have produced a video featuring the bug:
https://www.youtube.com/watch?v=SepjR-m1o5E