So, having read through that extremely long and largely uninformative article, I'm left with the impression that there's no real story of any substance here. The NSA spent a lot of time and resources trying to find any evidence to support Snowden's claims that he raised concerns about the legality of NSA programs but they couldn't find any, apart from a single email whining about a difficult question in a test he failed which even the most generous of interpretations would struggle to describe as "raising concerns".
In other words, the headline is a lie.
Ten minutes of my life I'll never get back.