As unlikely as it was, if anything went wrong during the mission did the United States have any protocols in place to prevent atomic weapons from falling into the hands of the Japanese?
Both bombs, Little boy and Fat man were fused for aerial detonation to maximise blast damage from the devices... From memory, both bombs were fused during the climb to bombing altitude, which would have meant that both bombs would probably have detonated in the air if the aircraft carrying them were shot down. Both bombs also had redundant contact fuses to ensure detonation if the barometric triggers failed.
So, in the event that the aircraft was shot down over Japan, the bombs would have detonated, ensuring that the weapons would not have fallen into the hands of the Japanese.