I had the same issue, went back to a stranded craft on the Mun surface from the tracking station after sending a rescue vehicle and found the first craft ~4000 m underground. I could still fly it there, though, upon exiting the 'surface' my craft quickly dissassembled (but wasn't technically destroyed). Weirdly enough, when my rescue craft arrived, it gave an accurate waypoint indicator for the craft position under the surface and it wasn't moving as far as I could tell. As soon as I changed to the stranded vehicle, it started falling with normal Mun gravity:
KSP Version 0.1.0.0.20892
Operating System - Windows 10prox64 latest
CPU and GPU models, Threadripper 1950X, RTX 2080 Ti, 64GB DDR4
Description of the bug.
Expected Behavior - Craft should rest on the planet surface while not attended
Observed Behavior - Craft was found not moving ~4000 m below the surface of Mun. Craft was still flyable, exited 'surface' of moon and was dissassembled
Steps to Replicate - save with craft landed on Mun, quit or switch to a different craft, return.
Fixes / Workarounds (if known..) - none
A list of ALL mods. none
Other Notes / Screenshots / Log Files : I have some, but haven't figured out how to upload them yet... I can't seem to use screenshots from my steam account