Honestly, there's nothing mysterious about Puma Punku, because our early ancestors already knew quite a good deal about archtecture, math and construction.
I believe what has made the image of Puma Punku change into a mystery and challenge, if I can put it that way, is the TV show Ancient Aliens where they claim the locals used serious tools tipped with "diamonds" and alien technology to construct these sites.
However, what they mention to say is, that our ancestors where masters of building complex structures such as the Pyramids, the Wall of China and many others.
Modern scientists have a problem to admit into history and science alike what doesn't fit their version of what evolution should be, that's what it's all about.