WSWS has a nice analysis of the NYT's handling of the Babchenko lie: https://www.wsws.org/en/articles/2018/06/01/pers-j01.html

Quotes:

"In their coverage, the Times and other major newspapers relied on a script they have used repeatedly: A prominent critic of the Kremlin dies or is injured abroad, and Moscow is immediately blamed. Any effort by Russia to deny these claims, or even to challenge the accusations, are treated as more evidence of a malevolent Kremlin plot."

and

"... the Times sought to shift the story to the Kremlin’s “denial machine,” instead of what the incident has exposed about the lies peddled by the Times. What really stands exposed is the propaganda machine operated by James Bennet, the editorial page editor of the Times, who manipulates the news in the service of the intelligence agencies to promote war abroad and political repression at home. For Bennet, when one lie is exposed, the time has come to reply with an even bigger lie."

Good article, worth reading.