A long time ago, one of my rocket (i.e Burning Star I ( https://www.simplerockets.com/c/7uzx9c/Burning-Star-I )) started having a very big issue: It always, and I repeat, ALWAYS ditched the rest of the rocket on start of the simulation. Then, a day later, I made another rocket: The Marduk I ( https://www.simplerockets.com/c/CuaRIy/Marduk-I ), that suffered the same problem. And now, I got a big SSTO, carrying a small vacuum-optimised rocket via a docking port, also suffering from that, but instead of ditching a stage, it undocks the rocket. I do not know how to reproduce, or how to really explain any of it.
In my HLV9 this also happened. The interstage isn't strong enough and unable to keep the rocket from falling which made the situation very awkward.