They have a database that says we have X, they have wallet addresses that say they have Y, due to crap programming they really have Z. Because they have a bunch of addresses with dust that can't move and a bunch more with such small amounts that even at 1 sat / byte it just does not pay to move them.
This is possible, especially as in certain places they work with less digits after decimal point (was it 5?) instead the normal 8 (where I would use actually 9 to be on the safe side).
But:
* I don't think that those satoshi make much of a difference, even if it's for audit
* it's clearly not a good enough reason for such high fees for so many tx, they could have been doing it with minimal fee