In short, the hyper-partisan 'paper of record' was operating in bad faith.
It's wasn't just the Times either. CJR's findings accurately reflect what most objective thinkers have known this whole time - they were all operating in bad faith.
That said, CJR aimed the majority of criticism towards the NYT.
"No narrative did more to shape Trump's relations with the press than Russiagate. The story, which included the Steele dossier and the Mueller report among other totemic moments, resulted in Pulitzer Prizes as well as embarrassing retractions and damaged careers," wrote CJR executive editor Kype Pope in an editor's note.
The findings were published in a lengthy, four-part series. The first section begins with a story about then-New York Times executive editor Dean Baquet's reaction when he found out Special Counsel Robert Mueller didn't plan to pursue Trump's ousting, telling his staff "Holy s---, Bob Mueller is not going to do it." -Fox News
"Baquet, speaking to his colleagues in a town hall meeting soon after the testimony concluded, acknowledged the Times had been caught 'a little tiny bit flat-footed' by the outcome of Mueller's investigation," according to Jeff Gerth - the author of CJR's lengthy retrospective.