Thanks for your answer, after looking at the video again there was a 1 second difference between the play clock and game clock. That is, there still was actually 1 second on the game clock when the 40 second (play clock) hit 0, and the clock/scoreboard operator let it run down to 0 as well and no one ever said anything or asked any questions. But if someone had noticed it should have been a delay of game on the offense and a 5 yard penalty with one last play on 4th down? It wasn't like the game was out of hand, they were only up by 2 points.Snapping the ball and the QB kneeling takes time. The QB can hesitate. There is no rule requiring him to instantly kneel.
When the QB kneels it takes time for the officials to blow their whistle and raise their hand to signal the end of the play.
When a play ends the 40 second clock does not start for the next pay instantaneously. There is always a slight hesitation.
If that happens 3 times could it add up to 12 seconds? Sure.
I don't see any errors or rule violations by the officials or clock operator in your scenario.