As long as the clutch pedal assembly is not coming apart (as used to happen on Polos) it should be okay. The Up is a cheap car, build down to a cheap car price. It's not a limo. Gearbox quality varies ...

A sharp clicking noise from under the dashboard when you press or release the clutch is almost certainly going to be down to a sticky or dry clutch-pedal pivot. It could also be the clutch cable ...

The garage is correct, the Citigo/Up/Mii does not have a great deal of soundproofing and this means you tend to hear every click and clunk in the cabin. The sound could be the carpet catching the ...