Same issue here. Happening on Minmus to Kerbin SOI change. Happened to different crafts that were very simple. I'm running KAS, and the first time I had situation where I attached an engine to crashed ship on Minmus, and I just chalked it up to something weird in the mod. Reloaded quicksave multiple, then finally attempted to take the engine off and reattach while in orbit. That seemed to work.
But then I went back with a ship fully assembled in the VAB. Landed on Minmus, did the science, left to back to Kerbin. Hit the SOI change and boom. So I did what someone else suggested and tried to time warp through the SOI change. That prevented the explosion. Give that a shot if you didn't already.
