Not a design flaw. It will happen in just about any a/c system from the condensation. My Civic did it, my Xterra did it, the Suburban did it, the Yukon does it, the GTI does it...
But, it's easy to work around: just switch off the a/c and keep the fan running for a few minutes before you shut down the car. That gets rid of any moisture in the system so it can't sit and mildew in there while the car is shut down.
If it's too far gone, you can buy cans of stuff at Cdn Tire to spray in the air intake that will kill the mould and freshen up the sytem. I've used it with success in the past, but if you don't do the a/c shutoff trick mentioned above, the smell will eventually come back.