I'm a Silva fan... but that's rubbish. Silva is one of the greatest fighters of all time. He will go down in history as one of, if not THE most dominant champion in the history of the sport.
Silva was in trouble during that fight. He was being controlled, taken down at will, punched in the face at will, and 2 minutes away from soundly losing the fight. Was he in trouble as far as the fight being stopped? Not really. Was he in trouble of losing? He sure as hell was.
Also, Sonnen may have not many tko's on his record, but the dude is strong as hell. A guy like that pounding on you is always the right couple punches away from ending a fight... especially when you're in his zone of expertise. I'm not talking about a lucky haymaker.
In my eyes, In a 5 round fight, once you get to the end of the 3rd round, having clearly lost all 3 rounds, then you are in trouble.