I think you are confusing the flow of money with the total budget. I think the numbers reported here are looking at individual transactions that can easily add up to more than a trillion dollars.
I'm not confused. The article states that they had 2.8T in adjustments on a ~500B budget. That is totally insane. That the aggregate averages of all those adjustments are 500% of each and every adjustment is inconceivable. Even the most incompetent organizations are not off by that kind of percentage over ALL of their adjustments.