Nobody seems to be arguing it is improper to point out bad calls to officials through appropriate internal grievances. It is coaches or players lamenting the bad calls publicly that detracts from the game. Those complaints usually are played to the tune of "we would have won the game but for this or that bad call," either expressly or implicitly. And unlike the exception in the Broncos-Bolts game where the ref actually admitted he blew a call, most so called bad calls are arguable.
Any complaints raised in the games you cited received the official statement "right call." You and I may disagree with the official statement, but fans can always complain about blown calls. Fans of opposing teams will point to the Colts "mugging" complaints in 2003 as proof the Patriots get away with calls as well. That is a fan debate, not a head coach-NFL debate that makes it appear to the public like officials are incompetent, biased or corrupt.