This dude's been doing an entire series on bad clock management. Yes, Coach McCarthy has been featured.
The most recent one is about the Bengals/Ravens game. My best guess is that it's just way harder to manage the clock when you're actually under the gun in a real game. But isn't this something that they practice? Don't they do drills on it in training camp? Maybe someone such as an assistant coach, or even some kind of observer, could give them the scenario and keep track of the clock. It would be like:
"You're down by 4 points and there's a minute and 37 seconds left. You get the ball on your own 12 yard line. You have two timeouts."
Maybe they even have an actual clock installed on the practice field. They could run scenarios like that and be evaluated on how well the coach handled the clock. Maybe even do it during a scrimmage. We practice that in the scrimmage for the Cowboys handling the clock, and then as a courtesy, we help the other team practice it. Some others mentioned practicing it in Madden. That probably wouldn't hurt. Do that, but I would also actually practice it in training camp with a real team, and then during a scrimmage would be even better.
Here's that dude's video on the topic.