Did the commander write the report or not?
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.
The commander did not write the report. It was done by a member of his staff. We do not know the context, nor the complete substance of the report. All we have is what snippets Ricks got from leakers.