First off, from Newtonian physics, there is nothing that says the train must be stationary at any time during the collision. Instead, physics says that the train must only decelerate as a result of the collision, such that the forces on the fly and the train are equal, as per Newton's 3rd Law, "for every action (force), there is an equal and opposite reaction (force)." Since the forces on the fly and the train are balanced, and since force equals mass times acceleration (Newton's 2nd Law), the negative acceleration (deceleration) of the train is tiny because of its tremendous mass. Actually, the splattering demonstrates that this is a completely inelastic collision, and for any collision, the conservation of energy is the overriding rule - K.E.fly + K.E.train = K.E.fly+train + Esplat (heat energy lost to smooshing the fly) - though the resulting deceleration is still miniscule unless the fly's velocity is sufficiently great to give it significant kinetic energy (K.E. = one half mass times velocity squared).