Could be a few things.
--How big is your tank? Rule of thumb is 10 gallons per inch of shell. So, if your turtle is 4 inches, you should have a 40 gallon tank. Bigger is always better with turtles though, so if you can go bigger, you should. Maps can grow anywhere from 5-9 inches (male) and 8-11 inches (female), so eventually you could need 100+ gallons, depending on the sex.
--Do you have the correct lighting? Turtles need both UVB and UVA light to grow and Develop properly. The fact that your turtle's shell is flaking tells me he might not be getting enough UVB. Some basking spot lights have UVB, but most don't. A lot of times you need to invest in 2 bulbs; one for heat (UVA rays, most basking bulbs are UVA) and one for UVB (try and stay away from coil lights if you can; a tube bulb is your best best. UVB rays help with the metabolism of calcium, promoting strong shell growth).
--Is your set up correct? You need two areas out of the water that the turtle can access and dry off completely. One of these spots needs to be directly under the heat lamp (6-11 inches away from the lamp itself), and one needs to be out of the light completely so the turtle can get out of the water and not be forced to bask. Gravel is not recommended, as the turtle might thing that it's food and try to eat it. Big stones are ok, as long as the turtle can't get stuck under them. Easier to clean, as well. A filter isn't NEEDED, but certainly is recommended. Turtles can be very dirty little things. If you go with a filter, go with one that is used for at least twice as much water as you have (canister filters are normally the best bet).
--As far as the food goes, fruit is not part of a turtle's diet. Not even for a treat. The sugars in fruits are hard for a turtle to metabolize, so stay away from them. Turtle pellets are good as a staple, but you need to add some variety as well. Baby turtles need extra calcium to help with shell growth. Small bits of liver dusted with a calcium supplement is a great way to add calcium into the diet. Another thing you can do is purchase a cuttlebone, which is essentially all calcium, for your turtle to chew on in between feedings. Veggies are more important when they get older (think 5 inches or bigger). Dark greens, like spinach, kale, or dandelion greens are a few examples. If you chop it up, they eat it like their normal food.
So, in short:
Make sure the tank is the right size, get the right lighting and set up, and feed more calcium and your little guy should bounce right back.
Good luck! =)