As donley posted, a credit card holder can dispute anything -- which doesn't mean that the credit card company will decide in the holder's favor. As far as I can tell from your post, you fixed the clutch and the clutch works but there are other issues with the car which he chose not to have repaired.
Charge backs can be a hassle to businesses -- especially small businesses which need the cash flow. I have some friends who sell stuff on a small scale and a disputed charge can really mess up their income if they were relying on it because every credit card company will put a hold on the funds until the dispute is resolved.
Some days I pray for Silence, Some days I pray for Soul,
Some days I just pray to the God of Sex and Drums and Rock 'N' Roll.