For some reason, I have been acquiring enemy ships and designs, I'm not sure why or how, just that I hate it. These enemy ships auto-refuel, and very slow, and generally have no jump drive, and worst of all, some of them auto-dock.
This clutters up my ship count, I generally keep it at 5000. Over half of my fleets ends up being enemy ships, intercepts and bombers, and hunting them down and telling them to undock and scrap is very tedious. But this is how I found the bug. When a planet is wiped out, buildings remain sometimes, ok that's fine. But it also leaves ships docked inside that can not be accessed again until colonized. Which makes me wonder about planets I've blown up, if those ships are permanently stuck in my ship count? But that's not a bug I'm concerned with.
When searching and undocking captured enemy ships from "MY" planets I occasionally found HOSTILE ships exiting my planets, often times thanking the planet for releasing them in the only way they know how, exterminating it.
There needs to be a better searching/sorting option when searching for planets with ships docked, And a way to command said ships to leave the dock and perform orders, without explicitly telling them to undock.
Also when a planets civilization is killed off or the planet is destroyed, all ships should immediately deploy from dock or be destroyed.