I wouldn't be surprised if the bulk of it was used in various "black op" programs and they just got a little sloppy with their bookkeeping entries. Either that, or it went to programs with such a high degree of secrecy attached that they don't do any bookkeeping at all for them. (No joke. There are classified government programs for which no records are kept.)
And even excluding all the weird Area-51 type stuff, there's still the situation of not everything on the government's books actually getting put on their books
Look how many years there were hundreds of billions spent on the War on Terror that never appeared on The Budget of the United States
. It was all handled "off book" and by direct executive order. I seem to recall hearing that could easily account for a few trillion in additional debt should they ever decide to "recognize" and "record" it in the formal accounting sense.Crime pays - and our governments love it.
Funny business to be sure. But with Washington operating the way it has since Regan took office, it's become "business as usual."