Guys, Pokéballs are not inherently technological devices. Sure, most fo them are nowdays, but remember that people used to put Pokémon into emptied fruits basically.
The thing all Pokémon have in common is the ability to change into the state of a pure energy being. However, in most cases, they just "snap" right back into their usual forme. Something about the inside of Apricorns prevents Pokémon from snapping back, which is why they can keep their energy form when trapped inside a hollowed-out Apricorn.
My best guess is that during the process of capturing both the Apricorn absorbs the "energy signature" of the Pokémon while the energy of the Pokémon adjusts to some properties of the Apricorn. Thta's the reason you can neither re-use a Pokeball nor "re-capture" a Pokémon. In the end, the technological Pokéball are merely devices to emulate the properties of an Apricorn. You don't need high-tech to capture Pokémon.
As someone suggested, I'd go with the same explanation that this process is much more difficult or even impossible if the Pokémon is fainted. Maybe it doesn't have enough energy to "impregnate" the ball. Also, Pokémon being energy beings, I also think that once wild Pokémon faint, they don't just lie there, but may be able to basically convert to energy quickly, then escape faster than you can throw a ball.
