Which I clarified in post #8, but I've now added an update to post #3.
One issue is what is meant when an object touches another object. If some part of the fly's body is considered to be in contact with some part of the train during the collision, then there's some moment in time where the point of contact is stopped with respect to the ground. If the situation is viewed from the molecular level, then there is no contact, just a repulsive force due to the electrons and their related fields, and the force from the field changes the direction of the fly's body, without actual contact, only slowing down the trains molecules without stopping them, although I'm not sure what happens to the average position of the affected electrons.
Then again even in a solid, the molecules are bouncing around and I'm wondering if the maximum speed of molecules between collisions exceeds the forward speed of the train, in which case, part of the train is moving backwards for brief moments even without external collisions.