The clock running down in the final 2:00 didn't bother me. In his shoes, I would want control of the time. Timeouts can be used to exert greater control over he clock when you possess the ball.
What I did notice was how negative Sean McDonough was of the decision to not call them. I've noticed his negativity before, too, and not just toward VT but toward a lot of coaching decisions. Anybody else feel this way?