Had recent incident where the lander, whilst travelling between planets, just happened to intersect another planet at same point, same time. Rather humorously, the lander travelled through the planet. Whilst I'm stoked I didn't lose the lander (and Commander!) I'm sure this isn't quite supposed to happen
I think that's just the nature of the beast. The "orbit" model is a simple one which is not actually taking into account the gravity (or existence of) all bodies in the system. I wouldn't expect this to change, unless maybe they decide to simplify inter-planetary travel altogether. (Like you build a beaming facility and simply teleport to the destination, skipping the interplanetary travel entirely.)
It happens rarely. It doesn't detect collision. Thinking how rare that has to be, no worries in my mind. I will consider it a "privledge" to witness it the few times it happens.
