Actually, presumably pygmie puffs didn’t exist in the first book
Pygmie Puffs are miniature Puffskiens, and those where doubtless around for years. And whilst you may reply that full size Puffskeins might have been prohibited, Puffskeins are not particularly big, and as such the laws would apply equally.
[The size of Puffskiens can be determined by the fact that a nest of them was found under the sofa at 12 Grimmauld Place, leading to the obvious conclusion that they’re not particularly big]