I have no idea how that mod works... also, because that mod is the one "Moving" stuff, ideally, he should be the one you report the bug to.
When it comes to multiple bodies, I'm actually just interfacing with an unused feature of the base game, uncontrolled bodies are a thing that is allowed to exist, and it tracked by the game's associated characters table
(my mod doesn't keep track of who owns what body, my mod simply changes controller and adds the previous body to the associated characters list, and then when you open the GUI, shows you the list)
In theory, ANY mod can do what I did, however, whatever space exploration is doing likely uses some scripts (that other mods can't intercept) to move stuff around, or even delete stuff.
it would be worth reporting to space exploration that associated characters are (Deleted? lose their association? what happens when there's an owned character in the rocket?)