Morgan Stanley suffered a setback when a federal judge ruled against it in a long-running legal dispute with hundreds of financial advisors seeking millions of dollars in deferred compensation they say the company has unfairly withheld from them.

Judge Paul G. Gardephe denied Morgan Stanley’s request to review a November 2023 ruling that the company said put it at a disadvantage in dozens of arbitration cases that advisers have filed against Morgan Stanley.

He…