I understand how this happens, especially with a coach who is running his offense. He's worried about the play call, the personnel, the adjustments, and more than ever before he calls the play while his team is looking over to him from the line of scrimmage after he's analyzed the defense. We're not thinking about any of that when we're watching on TV. We can just focus on clock strategy.
What I don't understand, is why they don't address the problem. How don't you have a guy standing next to him or in his ear from the coach's box whose sole job is to focus on clock/game management issues, without any concern of getting personnel on the field, playcalling, etc. ?
When Herm Edwards was coaching the Jets he had a bunch of clock management problems and was big enough to say "hey, it's a problem" and assign someone to the role. Coaches, especially these college dudes whose sideline is going to be disorganized due to youth, limited practice time, etc., need to address the issue.