Yes it stopped but restarted IMO prematurely before chains were completely reset.
I thought this myself. People all around me were screaming for a TO, but on a first down in college football, unless I"m completely cuckoo, the clock is supposed to stop until the chains are reset, which gives you plenty of time to get up to the LOS and do something. It seemed like that happened really fast, which added to the confusion.
This is a very easy learning situation though. Tim Boyle, if he's a smart QB, knows now, and forever, that when in doubt, and there are less than 30 seconds on the clock, get the team set, snap the ball, and down it somehow, spike it, throw it over a WR's head into the bench. Whatever. Get the clock stopped.
But I forgot to set the game to record, so I can't watch, but I wonder who the hell is operating the clock at our home field, and why we don't do everything in our power to help ourselves win games. A slow finger on the clock there, helps. And if you think it doesn't happen....you're not paying attention to football.