This could be explained more broadly by ‘somehow some of the script-created entities still lose their script ownership or otherwise get treated as population-created’ and might be related to another report (which also hadn’t been consistently reproduced yet, though I don’t think anyone got around to checking the later additions there) of ‘sometimes server-created vehicles spawn with population peds in them’ implying that somehow the game might think these are game-managed vehicles at some point.
There was also another fix that got reverted shortly after as it regressed in hard-to-test ways so that might be the same issue as Vehicles created server-side using CREATE_AUTOMOBILE are not persistent - #8 by d-bubble as well.