When then-Secretary of State Hillary Clinton was at the State Department, she and her staff often tussled with Sen. Marco Rubio (R., Fla.) over diplomatic nominees, emails released Thursday show.

In one episode chronicled in the emails, the Clinton camp needed the help of her now potential opponent, Mr. Rubio, to get a controversial nominee through a tough confirmation process. But Clinton aides and allies had their doubts about him. They worried about his intentions as he assured them that he had changed his mind about the nominee to be the ambassador of El Salvador—Mari Carmen Aponte.