This sentence does not make sense: "Both foundations make indirect investments such as index or mutual funds, whose managers may or may not invest in fossil fuels." 

You don't "make" an investment such as an index. You don't make an investment such as a mutual fund. You invest "through" or "in" these things.

Someone may invest in or through an index fund, but who makes an investment such as an index?

Either poor editing or understanding of the subject matter