Every military situation produces multiple reports. Some are highly optimistic, some are highly pessimistic, but it all depends on what, specifically, the writer is instructed to look at. If he is told to look ONLY at the status of the "insurgency," he cannot, by mandate, look at other aspects that may have an impact on the situation, but not be directly in his tasking. Moreover, since this is the NY Times, we don't know how many OTHER, different reports were also submitted---only the one that was curiously leaked, and which curiously conforms to the NY Times' view of the war.
Did the commander read the intelligence report before it was published?