It's true that Obama says that he was blindsided by the conduct of the IRS and that the Justice Department acted independently in obtaining the AP phone records. Although his not knowing brings into question the control he has over his administration. His initial response to the scandals was most certainly criticized for being too passive, even by his own former staffers.
Considering the tactics deployed by the Justice Department against AP journalists, and the shifting explanation of the Benghazi attack, can Obama still say with a straight face that his is the "most transparent administration in history?"
Judging by the magnitude of the issues Obama faces, this and many other questions could linger for months.