Clicking noise on clutch pedal/brake pedal.

Doesn't do it all the time. Clicking noise whether the clutch is engaged or not engaged, I can also feel it on the brake pedal. I took it to the ford dealer (mileage is 30,600) and they havn't gave me a answer yet. He said that if it's the clutch thats worn out that warranty won't cover it. If its due to a mechanical difficulty then the warranty will cover it. Ive owned the car for less than ninety days and of course the dealer Youngblood Motors in Springfield Mo, says just eat it.
02' V6 5sp.