The refs didn't stop the clock because of the punt team. They originally stopped the clock because a Webb player was asked to step of the punt return for either (blood, wristband, or shirt untucked). Then the clock started again and the Webb coach wanted to know why the clock was running but he waited until the 25 seconds were almost over. After that Ecs ran out more clock before punting. Anyway to make a long story short the refs, coach, and Ecs ran the clock and not an illegal formation.