Metal expanding and contracting causing a ticking sound is normal. Every car I've had does it and you usually can't hear it until you turn the car off because it's masked by the engine noise. Them saying the rust is causing the ticking sounds is BS. It has nothing to do with it. Doesn't the warranty have something about rust and such in it? Open up your warranty book and find it.

 

Does a aftermarket system tick?

 

I just got my MXP catback exhaust installed and no more exhaust ticking after driving! Something with the stock exhaust definitely is tick/crackle prone. I understand the cooling ticks after shutdown - but my car - as well as many other G's, would tick loudly in the mid-section of the exhaust (near YPipe) even while running/idling.