That seems pretty typical for a paper published in Nature. I thought it was meant to be good but basically every paper to do with disease or biology I've read in Nature over the past 12 months has been like this: it looks superficially scientific and when read carefully it just falls apart. They've also been suppressing critical commentary sent to them. The Flaxman paper was atrocious and they sat on a formal response that was sent to them about it for like 6 months.