You know how it says "there's no will to fight!" when you try to send out a fainted Pokemon? It's about will. A knocked out Pokemon has no more will. A Pokemon that's just asleep is still trying to battle, but its body is in sleep paralysis.
My guess is that Pokeballs have something in them that tries to subdue willpower, thereby catching them. But if there's no will, it has nothing to target and it does nothing.
Rate my fresh headcanon.
