One aide was quoted referring to Vice President Joseph R. Biden Jr. using the phrase “bite me.” Gen. James L. Jones, then the national security adviser, was labeled a “clown” by one aide, according to the article, and General McChrystal was described as reacting with disdain to an e-mail from Richard C. Holbrooke, the special representative for Afghanistan and Pakistan, who died in December.

The article did not directly quote the general as saying anything overtly insubordinate.

Its author, Michael Hastings, and his editors have repeatedly defended the article’s accuracy. Eric Bates, the executive editor of Rolling Stone, said on Monday that the article was “accurate in every detail.”

The Pentagon report disputed key incidents or comments as reported in the article.

“Not all of the events at issue occurred as reported in the article,” it stated. “In some instances, we found no witness who acknowledged making or hearing the comments as reported. In other instances, we confirmed that the general substance of an incident at issue occurred, but not in the exact context described in the article.”

In a statement later Monday on its Web site, Rolling Stone questioned the methods of the Pentagon inspectors, who interviewed 15 people but not General McChrystal or Mr. Hastings.

“The report by the Pentagon’s inspector general offers no credible source — or indeed, any named source — contradicting the facts as reported in our story, ‘The Runaway General,’ ” the Rolling Stone statement said. “Much of the report, in fact, confirms our reporting, noting only that the Pentagon was unable to find witnesses ‘who acknowledged making or hearing the comments as reported.’ This is not surprising, given that the civilian and military advisers questioned by the Pentagon knew that their careers were on the line if they admitted to making such comments.”