It's quite common for loose stones to get caught behind the brake disc. It's usually obvious when it's happened, with the wheel making a loud scraping noise as the stone grinds along the disc. However, more often than not, the stone will work its own way out.

On the face of it, a brake clean reads like an unnecessary money-making job for the dealer. However, given your low mileage, it might be worth doing if the discs have a lot of surface rust that could result to corrosion and surface pitting.