Here is my theory.
My theory is, when the Sorters reject a good bill it is making a 'phantom' bill in its place. So if it spits out a bill (example we will use a 20) it is also putting a 'phantom' 20 in the slot that then gets put in to the strap. Then the strapped bills will get moved around and put in a box, in a brick, or on a pallet.
The act of adding the strapped packs to a set like bricks, boxes, bags, and pallets, does some sort of check with the programing. This is proven by the fact when anyone gets a phantom item in a box all you need to do is put that box on a pallet to clear the phantom items. (Also works with phantom objects stuck to pallets by putting the pallet on a trolly)
So when we go to send that cash out, the 'phantom' monies have already been corrected in the strapped packs. I do not know how the program keeps track of it all, as I already know that this is a ton of asset tracking for me to understand with my limited game making knowledge.
This will also make it harder to track, seeing that the XXL sorter fails around 1.5% of the time.
TLDR: XXL Rejecting good bills may be making phantom bills, that are being removed when they interact with asset consolidation items like bricks, pallets, bags, and boxes.