Kerbal Space Program

Upon undocking the two halves separate and also stay together in a weird quantum state while staging symbols disappear. They move through each other, throttle works on both, but they do not gain distance, upon time acceleration they suddenly merge back in a jumbled mess, resulting in part fragmentation or explosion.

KSP 1.2.2.01622 windows 64bit on windows 10
http://www.warpology.com/k/bug/DxDiag.txt
http://www.warpology.com/k/bug/KSP.log (no output log found ???)
http://www.warpology.com/k/bug/Jool%205.craft
http://www.warpology.com/k/bug/quicksave.sfs (loadmeta also here)
http://www.warpology.com/k/bug/undock_bug.mp4

The configuration of the ship is different in the save than the craft file when the bug happens, because it already finished the Tylo part. Thus the plane was undocked, the crew module was docked to the main probe body part, and docked again with the plane, and later around Laythe the plane docked with the main body once it made it back into orbit.