-Nature is full of bogus, like all journals, if not more. The reason for its high impact factor isn't due to consistently solid papers all around, it's due to a few very high impact, foundational papers and a crowd of minor impact/shaky ones that were sneaked in by big shots and friends of the editors. Look up retraction rates by journal and prepare to be surprised.

-I don't think you realize the step it takes to actually write to Nature and say: "Excuse me, that paper you published is wrong and you should retract it." You're liable to alienate all of the authors as well as piss off the editorial board for pointing out that they let a mistake slip through. You should be prepared to face vigorous backlash, and be completely confident in your own results if you don't want the repercussions to overwhelm you. Many communities related to specific fields are small and niche, so making enemies with one team often means that you've actually cut yourself off a good part of that community. You should be prepared for awkward moments in conferences when you meet each other, incendiary questions when giving talks and scathing "anonymous" peer-reviews for your future submitted work. It's far easier to assume good faith, give the authors the benefit of the doubt ("yeah the implementation is buggy but what software isn't? The main idea is probably sound") and move on.

-I don't know about other fields, but in mine, there's an unofficial accepted consensus on a set of very high-profile papers that happen to be either complete bunk or utterly useless. Again, we're talking about Science, Nature, etc. These papers made a lot of noise when they came out years ago, and now no one in their right mind would base their work on them. Again, you can't just knock on Science's editorial board and go "Excuse me, that hyped paper from a very big shot is useless and you shouldn't have published it", so it's just something people in the community know and whisper among themselves. I guess it may seem strange to outsiders though.