Manafort pleaded not guilty Wednesday morning to the charges, which included money laundering, conspiracy against the US, bank fraud, and false statements.
Manafort appeared in a federal courtroom in Washington, D.C., even as Special Counsel Robert Mueller prepared for another court hearing Friday in Virginia.
On Wednesday, Judge Amy Berman Jackson scolded Manafort for making a public statement last week about Gates' guilty plea.
Manafort maintains his innocence, and said he would take his case to trial. She said if it happened again, she would issue an order to show cause as to why the order had not been violated. Gates changed his plea last week and agreed to cooperate with Mueller's investigation.
Manafort has pleaded not guilty to all the charges he faces, although numerous legal observers say he is under increasing pressure to strike a deal with prosecutors.More news: Dan Fegan, Influential NBA Agent, Dies At 56 In Colorado Car Crash
Charlie Gile reported from Washington, and Tracy Connor from NY.
Manafort faces a second federal trial in northern Virginia, where he was has been charged with 18 additional counts of bank fraud, money laundering and tax fraud.
Normally such charges would be consolidated in one court, but Manafort has refused to allow this, which might be a legal tactic meant to make Mueller's case more hard.
On Monday, federal prosecutors moved to dismiss almost two dozen other charges that Gates faced in Virginia. Charges also have been filed against 13 Russians, but they remain fugitives. "I understand the impulse", Jackson said. His arraignment in that court is scheduled for Friday afternoon, and there is no trial date yet in that case. In it, Manafort said Gates' decision "does not alter my commitment to defend myself against the untrue piled up charges in the indictment against me".
Jackson said the two cases have some overlap, and could create complications for scheduling and potentially conflicting rulings on what evidence can be used during the trial.
The charges stem from Mueller's investigation into Russia's meddling in the 2016 USA presidential election.