Are you talking about the Pentagon or the Fed? I haven't heard that about the Fed.
As to the Pentagon, from everything I've heard the record keeping is a huge mess and they simply don't have the systems in place to track all of the activity agency-wide.
That's changing as they invest in accounting infrastructure, and this first attempt at a real audit is a good start.
Everyone knew that the audit would reveal lots of holes, but I haven't seen any accusations of wrongdoing.
But they are losing more than their entire budget, at least in those years. That makes it sound like they were a conduit for some other purpose.
And that much money funneled through them would have to be “printed” or generated by the Fed. There won’t be any accusations of wrongdoing because that level of money disappearing has to be authorized by the top, for no doubt some ostensibly national security purpose. Year after year. This isn’t a rogue general padding his retirement.