Id be digging a bit deeper on this one.
It would be very unusual for the Clear coat to start flaking of any reasonably newish vehicle unless the vehicle has had a poor after market paint job carried out at some stage. I would be taking the car to a body-shop person for a second opinion, and if suspicions are likely that there are signs of body repairs carried out, engage an engineer to do up a report on the extent of damaged area.
From what you say regarding damage, its an extremely expensive rectification.
If you bought this 3 year old car, and there was bodywork carried out without you being informed, you would have recourse with the dealer you bought it from, and he in-turn would have to follow it up with the person who traded in the car having signed the " No previous repair" section,.