These and other incidents certainly suggest that the NYT needs to re-examine its standards and practices regarding sources, but to get a full sense of the problem you should take a look at the following from TPM's account of the reaction to the Sean Penn/Rolling Stone interview with "El Chapo":
New York Times editor Dean Baquet told Margaret Sullivan, the paper's public editor, on Monday that he "would have walked away from the interview." The newspaper's standards editor, Philip B. Corbett, said the paper does not grant "prepublication approval to anyone."Pretty much anytime you point out an issue with the New York Times' ethics or quality control, this will be the other half of the problem: The paper really does see itself as a gold standard, not perfect perhaps, but far better than any of its peers. This attitude effectively prevents any serious self examination let alone real attempts at reform.
Would have New York Times have published the Sean Penn piece? I have no idea. Have they recently published articles that gave sources an inappropriate level of influence and thus misinformed their readers? Unquestionably. What's worse, the Rolling Stone piece came with a disclaimer.
The New York Times simply leaves it to us to it figure out on our own.