This is related to the closed bug T1407, but only effects entities that despawn from overheating.
When a ship with docked entities overheats and despawns, it leaves behind it's docks as ghose entities. The entities still show up as a turret or docked entity in navigation, and any weaponsfire goes right through them. reloading the sector (by restarting, or leaving then coming back) will fix the docks.
This is an issue because the ai will target these unkillable entities and become useless in a battle due to it. This causes a lot of problems for fleet battles where the ai will target these ghose entities and be unable to make any progress on killing them.
I have not filled in the java, os or video card information, as I'm fairly certain this isn't os specific, so I think such information would be a distraction. If you are unable to reproduce, I'm happy to provide more information about my setup