And the "debunk" sites clearly explain, what he meant by that was that the Pentagon literally could not account for that amount of money. Not that trillions of dollars were missing, but that their accounting capabilities were not sufficient enough to track that large of a sum of money.

As mentioned, the entire US budget was less than 2 trillion dollars in 2001. That would be an awful lot of money to go missing and no one notice, 9/11 or not.