This is the result of a famous Harvard Kennedy School study that came out in April.
According to Brian Stelter in the NY Times: "The New York Times characterized waterboarding as torture in 44 of the 54 articles that mentioned the practice from 1931 to 1999. The Times called it torture or implied that it was torture in two of 143 articles from 2002 to 2008."
Stelter also has extensive quotes from Bill Keller, the executive editor of the NYT. It's embarassing in that it does not include a mea culpa. This was an obvious mistake, even understandable. They might not have been aware they were doing it. What's not understandable is that, once caught, Keller starts spinning.
Adam Serwer, writing in the American Prospect, summed it up as I see it. "It's a good rule of thumb that anyone responding to a criticism by accusing someone else of enforcing 'political correctness' is factually incorrect. That's because if the actual facts of the criticism were in dispute, they'd dispute them."
There's been much comment on the piece, as you would expect.
My own two cents. I come from a profession, software development, where we actively seek out our mistakes. We have formal processes for it. We teach our users how to report the mistakes, so we're more likely to understand what they're saying. We'd be nowhere if we tried to deny or spin them. Bugs could never be fixed, processes could never be corrected, we'd never move past the mistakes we made in the past.