The NY Times hasn't exactly been completely honest in its reporting on the war.
I don't think that's what they were saying. It seemed more like they were saying "If you don't pay us, we can't pay them, and they'll stop working."
One type of contract vehicle is Cost Plus Incentive Fee (CPIF), which bases a portion of the negotiated fee on performance criteria. That's pretty typical for ID/IQ (Indefinite Delivery/Indefinite Quantity) contracts. (And leave it to the NY Times to describe a standard method of government contracting so that it sounds nefarious.)
The part about the DCAA role was one I would have liked to have seen more information on. If there's any substance to the issues raised in the article, it will be established there.
However, I agree completely that combat units should have their own mess sections.
(Just to illustrate that there may be more than meets the eye: Years ago, a subcontractor had completed all terms of his contract. The managing civil servant demanded additional, uncompensated work out of the sub. He directed me to withhold payment until the additional work was complete. (He also raised hell with my boss when I ignored his direction, but that's a different story ...))
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