AIUI, the Pentagon failing an audit is essentially akin to most people failing an audit because they can't produce every single paper receipt for everything they've ever purchased. Combine that with the fact that the Pentagon is (I believe) the single largest purchaser on the planet, the fact that much of what it does is compartmentalized in different security buckets, and that the managerial staff tends to be younger than most organizations, and it shouldn't be so surprising that it's persistently in a state of being unable to literally dot every i and cross every t.