Nature is just as susceptible to the perverse incentives at play in the academic publishing market as anyone else, and has had their share of controversies over the years including having to retract papers after they were found to be bogus.

In and of itself, "Being published in a peer reviewed journal" does not place the contents of a paper beyond reproach or criticism.

Peer review is not designed to combat fraud.

From personal experience: in Nature Communications the handling editor and editor in chief absolutely do intervene, in my example to suppress a proper lit review that would have revealed the paper under review as much less innovative than claimed.