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Right, so this theory is pretty weak, I've been sitting on it for years since X and Y came out. I was waiting for potential X and Y sequels to perhaps give us more information to go off of, but that isn't happening so oh well.
The theory is that Foongus were first created in Laverre City. There's not a lot to go off of but there's some evidence. First of all, Laverre City is absolutely covered in mushrooms, specifically red mushrooms with white spots. This isn't surprising, that's amanita muscaria. It's the most well-known mushroom in popular culture and has historically been a symbol of strange magic, and doubly often is depicted with fairies. Foongus is based on exactly such mushrooms, and the game designers placed wild Foongus on the route directly east of Laverre. (You can't encounter wild pokémon in the city.)
So already you can see they intentionally made it so Foongus were able to be found next to Laverre. This might be for other reasons than just attention to detail, however. The Pokédex states that no one knows how Foongus came to resemble a pokéball. Now the only other clue to this theory: there is a Pokéball Factory in Laverre City. Is it not slightly suspicious, that the very place pokéballs are manufactured in Kalos, is the same area with tons of mushroom and wild Foongus?
The theory is that some sort of fairy-magic-bullshit went down a long time ago, maybe some local mushrooms fell onto the conveyor belt, or a batch of defective pokéballs were dumped in the forest next to some trees. But somehow, the Pokéball Factory lead local fungi to mutate into Foongus.
