There's no question that the errant whistle by the officials on a potentially huge play by Danny Amendola changed the landscape of the game. Bills head coach Rex Ryan ran in front of the official on the sideline, causing the official to blow his whistle while Tom Brady was still active and throwing the ball in the field of play.
Amendola caught the pass and had just one man to beat down the field for a touchdown, but since the whistle had been blown he could not advance the football.
This series led to a missed field goal by Stephen Gostkowski and a subsequent rushing touchdown by the Bills. It was a 10-point swing.
The whistle was absolutely ridiculous. What isn't ridiculous is how the officials handled the ball placement after the error had already been made.
Rule 13, Section 1, 13 ARTICLE 8. NON-PLAYER PERSONNEL. Non-player personnel of a club (e.g., management personnel, coaches, trainers, equipment men) are prohibited from making unnecessary physical contact with or directing abusive, threatening, or insulting language or gestures at opponents, game officials, or representatives of the League.
Penalty: Loss of 15 yards. (Unsportsmanlike Conduct.)
Enforcement is from:
(a) the succeeding spot if the ball is dead;
(b) the previous spot if the ball was in play; or
(c) whatever spot the Referee, after consulting with the crew, deems equitable. (Palpably Unfair Act.)
Basically, officials have the prerogative to enforce the 15-yard penalty to Rex Ryan from whatever spot they deem equitable. The fact is that Brady completed the pass to Amendola, but that there was still a defender to beat. The officials felt that, regardless of the ball being dead at the time of the whistle, placing ball at the spot of Amendola's reception would be the fair decision, and then tacking on 15 yards.
The whistle was a terrible call, but the officials followed the book after the error was already made.