Pokémon - pokemon logic

Rayquaza didn't do shit because it is locked away in some kid's pokeball

Simple Rayquza is guardian of the Ozone, so when something tries to enter through it's territory Rayquaza makes an effort to stop it.
But then something just wormholes in to the ground level it's not Rayquaza's problem, the earth isn't Rayquaza's domain, it's Zygarde's domain and Zygarde's problem now.