In the fourth quarter of the game, Peyton Manning threw a pass that went incomplete to bring up a 3rd-and-12 with 8:25 left in the game. The game clock was stopped at this time because of the incomplete pass. But the play clock was set to 40 seconds for the following play per usual. The play clock ran down to nine seconds and then paused. It was then reset to 25 seconds, giving the Broncos extra time.
Here's video of it. Note that it pauses at nine seconds and resets to 25 seconds.
It does seem weird but this was actually by the book. What happened was, according to a league official, a strong wind blew the ball off its mark on the line at around the nine second mark. The ball was reset at the line of scrimmage and the play clock was reset to 25 seconds, "which was the proper mechanic in this situation because the game clock was not running after the preceding incomplete pass," according to a league official.
So, no, Peyton Manning does not control the play clock.