Most of those problems stem from the lack of property rights. If a company cannot sustain its business with what it owns, then it should go out of business. However, non-market forces prop up these unsustainable businesses or turn a blind eye to the destruction of the commons. They "steal" from the rest of us via subsidies or abuse of public resources. Those are not market failures, contrary to popular opinion.
Things like the atmosphere, food web, water cycle etc. are fundamentally different than ownership of physical objects or even land. They are not confined to a particular place, and being fundamentally diffuse transactions and interactions with them are not obviously subject to singular control. Even if you break them down into components the bookkeeping and transaction cost is far too high.
Saying that they're not market failures says more about the narrow definition of "market" than about the workings and evolution of capitalist systems (including both visible systems like farms and factories and invisible systems like laws and power structures).
