Getting a handle on a government-wide program is a monumental task. And, if the program makes the management of the agency quicker and easier, there is not much incentive to make changes.
A good example is the recent GAO report on government purchase cards. In its summary, GAO says that it "asked agencies to provide documentation on selected transactions to prove that the purchase of goods or services had been properly authorized and that when the good or service was delivered, an individual other than the cardholder received and signed for it."
That sounds simple and straightforward and a decent system of records should have provided the information.