Yes, there was his part in the selling of the WMD narrative in Iraq:

On February 11, 2003, one month before the U.S.-led invasion of Iraq, Mueller gave testimony to the Senate Select Committee on Intelligence. Mueller informed the American public that "[s]even countries designated as state sponsors of terrorism—Iran, Iraq, Syria, Sudan, Libya, Cuba, and North Korea—remain active in the United States and continue to support terrorist groups that have targeted Americans. As Director Tenet has pointed out, Secretary Powell presented evidence last week that Baghdad has failed to disarm its weapons of mass destruction, willfully attempting to evade and deceive the international community. Our particular concern is that Saddam Hussein may supply terrorists with biological, chemical or radiological material."[48][49] Highlighting this worry in February 2003, FBI Special Agent Coleen Rowley wrote an open letter to Mueller in which she warned that "the bureau will [not] be able to stem the flood of terrorism that will likely head our way in the wake of an attack on Iraq"[50][51] and encouraged Mueller to "share [her concerns] with the President and Attorney General."

But he did oppose the renewal of the warrantless wiretapping:

On March 10, 2004, while United States Attorney General John Ashcroft was at the George Washington University Hospital for gallbladder surgery,[52] then-deputy attorney general James Comey received a call from Ashcroft's wife informing him that White House Chief of Staff Andrew Card and White House Counsel Alberto Gonzales were about to visit Ashcroft to convince him to renew a program of warrantless wiretapping under the Terrorist Surveillance Program which the DOJ ruled unconstitutional.[52] Ashcroft refused to sign, as he had previously agreed, but the following day the White House renewed the program anyway.[52] Mueller and Comey then threatened to resign.[53] On March 12, 2004, after private, individual meetings with Mueller and Comey at the White House, the president supported changing the program to satisfy the concerns of Mueller, Ashcroft, and Comey.