Yes, it's an issue with almost all cars, and I have run into it before, but I have not had any problems in over 10 years now that I know how to keep it from happening.
When you are using the A/C, don't leave it on recirculate all the time (recirc makes the system work harder). Turn off recirc after the car has cooled down.
And a few miles before you reach your destination, turn the A/C off, but LEAVE THE FAN ON. Leaving the fan on for a few minutes will help dry out everything inside the system, and keep away the musty smell.