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In fairness, the Metroids in Prime were all on one frigate, which is the one that crashed on Tallon IV. They were the ones that were evacuated from Zebes before Samus tore the whole place a new ass.

I kind of forget where they were supposed to come from in the other two games but I believe Dark Samus had something to do with it - since Dark Samus was a Metroid that had become a Leviathan Guardian, it makes sense that she could spawn Phazon-based Metroids.