We know the brain doesn't do "backpropogation" in the sense that backpropagation is a complete description of how the brain works. It may be a component, but there has to be much more, because what backpropogation can do is fairly well characterized mathematically now and is not sufficient to build anything like a human brain. If you haven't seen a paper that clearly spells that out, it's because it would be considered too trivially obvious a result to publish.

When we don't know how a thing works that does not preclude us being able to eliminate some of the possibilities. Our ignorance is profound, but not total.