It could be fungus growing on shell. I've heard you can soak them in salt water for 15 minutes while scrubbing the areas with a clean toothbrush once a day until it goes away. If that does not work after a 2 weeks you should take the turtle to a vet that specializes in reptiles... Hope that helps. :)
Most likely it is the starting of shell rot. Do not soak the turtle in salt water as it is not a salt water animal. You can use salt water (saline solution) 1 tbl spoon salt to 2 cups water and use a q-tip ir soft tooth brush to clean the area, the key thing with shell rot is to keep the shell clean and dry, so if it is an aquadic turtle (which I'm sure it is) this means keeping out of water for most of the time until the shell is healed, you can put it in water for about 2 hours a day so he can drink and exercise. Another great option is betadine solution, using a q-tip you put the betadine on the effected area and leave it on to dry, doing this 3-4 times a day, works way better than saline.