I’ve seen others propose Dark Samus killed them as competitors, but I’m unsure.

Its pretty clear from later entries that the meteor in Metroid Prime (the game) was probably unhealthy/diseased. I suspect orange phazon is not produced by healthy Leviathan seeds and why it, and thus orange phazite are so rare.

I’ve also suspected that the reason Metroid Prime could create phazon (which it then allowed to self-replicate/corrupt normal matter and farmed like leafcutting ants do with fungus) is that the diseased core, or pieces of it fused with the metroid it had made into a guardian. Just as pieces of  the pulped metroid prime later fused with the Phazon Suit. 

Thus the remains could be Dark Samus’s  failed attempts to create kin for herself, end up failing because the original metroid prime was unique and unreproducable. Metroids become social organisms in some ecosystems, and phazon mutation seems to increase their sociability. Behind the visor of Dark Samus could be a well of loneliness. 

Her attempts then sortof mirror the failure of the pirates to create Dark Metroids not knowing it would require ing.