This is a pretty lousy rule which....
...COULD have cost the Texans the game. It didn't turn out to make a difference, but it could have.
Texans lead the Bengals 19-13 with 2:40 to play. Texans have the ball 3rd and 2 and the Bengals are out of time outs.
Houston completes a pass over the middle for the first down. That should allow enough time to pass until the two minute warning where the Texans probably wouldn't even have to run a play. With a 1st down, 2:00 to play and no Bengals time outs, you can basically run the clock out.
But the Bengals were flagged for a helmet to helmet hit with about 2:30 to play. Yes, it gave Houston 15 yards but it also stopped the clock which wouldn't resume until the ball was snapped. So instead of hitting the two minute warning with a 1st down, the Texans reached it on 2nd down.
So the penalty basically traded 15 yards for an extra timeout. Because of the penalty, the Texans couldn't run the clock out without getting another first down (which they did). But if they didn't, the Bengals would get the ball back -- and the helmet-to-helmet penalty will have benefited the offending team since it gives them a chance they wouldn't have had without the penalty.
That seems pretty rotten to me. I don't see why, in that situation, that the clock shouldn't start running when the ball is respotted and the play clock then starts to tick. Defensive penalties should not be allowed to stop the clock on a play where the clock would otherwise continue to run, especially in the last 5 minutes when the defensive team is out of timeouts.