When Judge Jed Rakoff refused to sign off on a $285 million settlement between the U.S. Securities and Exchange Commission and Citigroup Global Markets Inc. last week, his decision reverberated beyond the securities bar.

The Southern District of New York judge took aim at the SEC not so much for the penalty — though he found it lacking — but because the settlement would have let Citigroup off the hook without admitting or denying wrongdoing in connection with a failed mortgage-backed securities fund.