Bowles obviously just screwed up and didn't pay attention when he got his timeout back. There have been several instances in recent history of playoff games flipping with almost no time left. Chiefs 13 seconds left... Diggs! Sideline! Touchdown! Unbelievable!
Not something that would get him fired but the game ain't over till it's over. "Gentlemen agreements" don't exist when you're facing either elimination or an NFC Championship birth.