I always assumed that it was a glitch in the trading system. I always imagined it works in a similar manner to how some portray teleportation, where they split what's being teleported to the very molecules and reconstruct it, only with some Pokémon, if they are or unless they aren't carrying a specific item, the teleportation machine glitches out and creates a mutation.

Also unrelated, but damn, the Winnie the Pooh movie is an untapped goldmine of reaction images.

That's a rather nice way to put it storywise, but still a dick move on the devs' part for all of what it is.