Same problem here. It happened to me when i was timewarping for a Mun Insertion Burn from Low Kerbin Orbit and again when I was undocking a Duna Lander from a mothership and the two had gotten squished together.
https://imgur.com/a/YhFtigo <----- This is an Imgur Link to the unwanted partclipping with my Mun Rocket. (I do not have photos of the Duna mission)
Very annoying if you want a craft that rearranges Apollo-style. Reloading SaveFiles does not change anything unless the compression occurred after the save was made.
