He did...on charges against Trump, a sitting president.
"When it came to the president’s culpability, we needed to go forward only after taking into account the OLC opinion that indicated that a president, a sitting president, cannot be indicted."
Robert Mueller, Testimony to Congress
However, Mueller did indict on 34 other people, garnering 8 convictions and 25 standing indictments for people who ran.
Mueller and Durham absolutely had prosecutorial powers the same as a United States Attorney. They could convene grand juries, prosecute cases, try cases.
And both did.