It wasn't that the stage separated and then collided with the engines of the next stage, but that the decouplers didn't fire when staged, something that I've not had happen before. I know what you mean about the "get it stable, then separate" method. I've even let a problematic vehicle drift for a couple of seconds to stabilise, then stage, then ease in the thrust a couple seconds after that, to avoid large tanks smashing into the next stage's engine.