In an interview with his biographer Stephen Hayes, published by the Weekly Standard, former Vice President Cheney laments Bush's decision not to pardon former Vice Presidential Chief of Staff "Scooter" Libby. From the WS:
Cheney told THE WEEKLY STANDARD that his former chief of staff, I. Lewis "Scooter" Libby, whom he described as a "victim of a serious miscarriage of justice," deserved a presidential pardon.
Asked for his reaction to Bush's decision Cheney said: "Scooter Libby is one of the most capable and honorable men I've ever known. He's been an outstanding public servant throughout his career. He was the victim of a serious miscarriage of justice, and I strongly believe that he deserved a presidential pardon. Obviously, I disagree with President Bush's decision."
The article also notes that Cheney only ever publicly disagreed with Bush four times while in office. The occasions involved a ban on gay marriage, Donald Rumsfeld's firing, the D.C.'s gun ban, and North Korea. Cheney's disagreement over the Libby pardon (or lack thereof), stated publicly just after leaving office, technically makes five -- though it doesn't really matter anymore.