The theory is that there was an older and more advanced civilisation that built them using more advanced techniques which are now lost.

And the Inca inherited pre-existing structures.

The Inca did do stonework of their own, but not close to the standard exhibited in this article.

Well, there's obviously the alien contact theory. If you've ever been to Nazca where the landing strips are only a few hundred miles from the Inca empire you'd be a believer. If you want to believe, that is.