I do plan on mentioning this later on once the kids start actually hatching out, specifically when Groudon and Kyogre's babies end up in Maple's care, she'll talk about how they're seriously messing with the weather and start wondering if they're doing the right thing with this whole breeding plan...
They will then ignore this and keep going anyway
Anyway, my point is that I do have plans to talk about the issues of having multiple Legends where there should only be one