They've always noticed something weird about gardevoir, marill, and jigglypuff, however it never fit into any previous type classification. Recently these pokemon have been using moves strong against dragon-, dark-, and fighting-type pokemon. This is an unusual occurance and nothing else fit into this, and as such a new type was created to classify this strange phenomenon.
So basically we pretend marill has been weak to poison, immune to dragon, and neutral to steel this whole time, but we didn't have a classification for this until now, and they haven't shown fairy-types moves to humans until now, but we figure they always had the capabilities.
alternatively if there's a time skip it could be some mutation that goes onto all marills to meet the demand of dark/fighting/dragons that are giving everyone in the wild shit, natural selection kinda thing
