When a play ends outside the numbers, the normal process is for the linesman or side judge to mark the spot with the ball and for a new ball to be brought in from the sideline. This provides a good reference for when the ball is placed on the hash. This doesn't always happen, especially in cases where time is short, but it is the normal procedure. The ball you see come in appears (based on the angle from which it comes) to be a new ball, and it appears to have not come in immediately. I don't know if Colorado had their own ball crew at the game, or if it Hawaii was running balls for both teams, but if you look carefully at the very beginning of the clip, it appears that the umpire is already signalling for a ball, and it took a while for it to come in. To be fair to the ball boys, they are instructed to look for the side judge first, who will usually come up field if the linesman is spotting the ball. They don't normally throw a ball directly to the umpire so he would probably have to get their attention.

Not saying that the refs didn't mess this up - maybe they should have stopped the clock when the ball went off of the Hawaii player.

As an aside, this is why you see more and more teams bringing their own ball boys to away games. It's pretty easy for the ball crew to affect the speed of play by delaying getting a new ball in. BYU has started using their own ball boys at away games since the implementation of GFGH.