Is it just an error in this game? Can their hitboxes overlap as one?

nope its when a fireball hits the gap of 2 flying koopas when they are together there fore you get lucky

also koopas have their own hitbox

Ah It was just lucky, not an error.. I see, thank you :)

The 2 Paratroopas were close enough together that you could shoot 1 fireball and it will hit both the Paratroopa's hitboxes.