Some of it comes down to agencies needing to protect themselves from congressional witch-hunts. Consider a congressman or political party that has ideological objections to an agency even existing and wishes to neuter or eliminate it. A stellar way of achieving this is by making the target seem wasteful and fraudulent [1]. If there is actual fraud, no matter how small or how much of a corner case, this task becomes even easier.
1. A good example of this is how Republicans periodically attempt to defund science agencies by mocking research projects that sound frivolous.
A Democrat, the late Senator William Proxmire of Wisconsin, was well known for mocking frivolous-sounding research projects. From the Wikipedia article[0]:
"In 1987, Stewart Brand accused Proxmire of recklessly attacking legitimate research for the crass purpose of furthering his own political career, with gross indifference as to whether his assertions were true or false as well as the long-term effects on American science and technology policy."
It's good to see examples from both sides. That being said, what the above mentions is Republican doctrine, as opposed to isolated cases of politicians(on either side) simply blindly furthering their political careers.
1. A good example of this is how Republicans periodically attempt to defund science agencies by mocking research projects that sound frivolous.