It is a strange surrender for science to describe Clefairy as "magical" - in truth, there is some explanation for all their strange attacks and abilities, just one which has eluded professors to this day. Their haunting, unearthly song, critical hit-preventing chants, immunity to status effects, and ability to sacrifice themselves to revive other pokemon surely have their own internal logic no less rational than our own. Scientists have surrendered because xenobiology is a bizarre field which requires old assumptions to be thrown out the window; Clefairy are so strange, so literally alien, that no one has come close to understanding them in the way which we understand how Charmander store fire in their stomachs for flamethrower.
And there is a great deal about Clefairy which suggests magic. The way in which they chant their name while moving their hands and making all sorts of attacks come to life was probably the inspiration for stories about wizards. To be fair, Metronome is chaos magic, not magic from spellbooks: it calls down a random technique which is as often useless or counterproductive as it is useful, and is used only in desperation. There is no such thing as a Clefairy which can summon fireballs.
But Metronome captured human imaginations enough that Clefairy dolls were made by the millions for sale as a magical totem. They have none of the powers which New Age hucksters claim, and are generally regarded by right-thinking people as a scam or a cute but overpriced decoration, but for some strange reason (which surely can be explained by science) they maintain the ability to scare wild pokemon away.