If they believe Manafort has something detrimental to the Obama regime and/or the FBI under Mueller, then indicting him was probably the worst thing they could have done. As a defendant in a criminal case he will be able to demand access to any and all documents related to the charges brought against him, and might even be able to subpoena the FBI agents involved in those matters.
... people make errors in their haste. It is entirely possible that they overlooked that.