If there is any bleeding at all or if you find any deep pits in your turtle's shell you need to see a vet right away because she'll need antibiotics.
My opinion is that if there is a chance that a shell is infected with bacteria or fungus then it's better to treat it rather than wait until it potentially gets a lot worse and threatens the turtle's life.
There are a number of recommended treatments for shell infections. Here are suggestions from another well respected site which recommends Acriflavine:
http://www.austinsturtlepage.com/Care/medshell.htm
Something that a lot of people on here recommend is another antiseptic called Hibiclens. Hibiclens is an antiseptic liquid hand soap for people. It's available in the pharmacy section of a store like Walgreens. It's similar to a hand wash used in hospitals. I used it on Spot's shell and he's almost completely well now. I like Hibiclens because it's easy to find, inexpensive (about $10 for a bottle that will last a long time) and effective.
Dilute a couple of tablespoons of Hibiclens with an equal amount of water. Get a soft toothbrush. Holding your turtle firmly over the sink, gently rub the Hibiclens solution all over her shell with the toothbrush. Be gentle. Drizzle a little of the solution in the arm and leg holes with your fingers so as to get some solution on the areas you can't reach with the toothbrush, being very careful not to get any on her head or face.
Your turtle will be slippery and wiggling so hold her carefully and near the bottom of the sink so that if you do loose your grip she won't fall far.
Then rinse her off very thoroughly with cool tap water. After I've rinsed my turtle thoroughly, I fill the sink part way with clean water and let him float in it for a minute just to be sure I've gotten everything off. The Hibiclens is a soap and will be very irritating if not rinsed well.
Repeat this every day for 10 days.
I think you should also dry your turtle out some. This is called drydocking. Since fungus and bacteria thrive in moist environments this helps with the cure. Get a box or big tub that your turtle can't climb out of. Put a soft towel in the bottom and get another to cover the top with. At night, put your turtle in the box to sleep and put the box in a safe, warm, dark place. Put the other towel over the top of the box. In the morning, the turtle goes back into the tank. Do this three or four times.
Different people on here do things a little differently. I hope anyone who has a different idea will please speak up and share their opinions with you too!