Its not a problem but a fact of life. Symbiotic relationships are most commonly parasitic. It takes a lot of evolutionary fine tuning for a mutually beneficial system to emerge. Plenty of things have gone extinct over the course of life due to other species doing. Perhaps the worst event was the great oxygenation event, when photosynthetic life emerged and polluted the earth with oxygen to the point of mass extinction of the previously dominant anaerobic life forms.

We humans are no different than what came before. We are a parasite to most species we rely upon. We pollute the air to the point that it harms other species much like earlier forms of life have done. Solving this 'problem' for good will amount to an evolutionary change in our species. I say problem in quotes because its only a problem for humans and any of the current crop of species making up the biomass on earth who are harmed by our actions. Extinction exposes opportunities for other phenotypes or species to take advantage of the earths resources at least. One thing that is certain is that life on earth moves on as always.