The corruption and rot that remains inside the DOJ is specifically because AG Bill Barr refuses to deal with it.  A result was the Roger Stone sentencing recommendation fiasco.
AG Bill Barr cannot admit rogue anti-Trump prosecutors defied his leadership because that would embarassingly highlight his own weakness and inability; so he blames President Trump.
Matt Whitaker notes how Michael Flynn and Andrew McCabe were charged with exactly the same issue, lying to FBI investigators.  Andrew McCabe is told he will not be prosecuted, Michael Flynn has had his life destroyed.  This is a big problem.