The Paige article basically says that Fox didn't like the series of plays which gave the ball back to the ravens. Fox basically admits that in that offensive series, running the ball 3 straight times was not the right thing to do. Fox says that the Broncos should have passed on 1st and 2nd down and then IF they still needed a first down, then on 3rd down, they should have at least lined up in a situation where Manning could audible and change the play at the LOS.
Good for Fox to realize that this situation that lead to the Flacco bomb and the OT loss were completely avoidable if the previous offensive series could have gotten 1 first down. Game over at that point.
But the shock of the Ravens bomb TD lead to the Broncos taking a knee at the end of the 4th quarter because, quite frankly, the Broncos were so shocked by the situation that they simply had to go into the lockerroom and regroup.