Brook Farm participant, ran an advertisement in the June 13, 1856 issue of the newspaper which caused a bit of a headache.
Sylvanus Cobb, Jr. signed a contract with Robert Bonner to write for his New York Ledger. Bonner always paid top dollar for talent and promoted his contributors aggressively. It surpassed the Tribune in readership and, by the fall of 1856, its success was celebrated with a hundred-gun salute at City Hall Park. Bonner advertised what would be Cobb's second serialized novel for the Ledger; the full-page ad in the Tribune cost Bonner $1,500 and took up a full page.
Dana, however, decided to throw in an editorial on the page next to the advertisement, roundly condemning the Ledger. Logically, it's not a good idea to criticize advertisers, especially one which is such a high-paying, high-profile client. Bonner was outraged, forcing the Tribune to print an apology. Dana later resigned from the staff in 1862.
Another member of the Tribune staff, George Ripley, was also a former Brook Farmer (and, in fact, its visionary founder). After his radical Utopianism and Fourierism, Ripley had mostly settled into a less radical figure and became a popular critic. In his criticism, unlike Dana, he rarely engaged in literary disputes and was known for being cheery, good-natured, and uncontroversial.
*I haven't been able to find either the offensive editorial in question or the apology from which to quote. Anyone with links to online resources, feel free to drop them in the comments section!