If you suppose the absence of supernatural factors, of course you cannot conclusively prove the supernatural. Any why does science assume there are not supernatural factors? Well, there are valid reasons, but to a theist that's merely a model of reality for the purpose of discovery and pedagogy.

But to take the premise as the conclusion is a logical fallacy. And on top of that, the underlying premise (assume only the physical and measurable exist) is a metaphysical premise and outside the purview of science.