Them it is most likely a form of shell rot. How wet is your substrate?
You'll have to do a complete change of substrate and clean the enclosure with somethinng that will kill bacteria and fungus. Let it dry. Rewash it again with an extra rinse. let it dry completely and then put in new substrate.

I wouldn't place the turtle back into the cleaned enclosure until you've gotten rid of the crud on the shell. Set up a hospital tank or rubbermaid container. Put dry newspaper in teh bottom. You can shred some for her to bury herself in. Put in a big water dish that she can go in and soak as needed to maintain her hydration.

For your turtle clean the area with a Chlorahexadine solution, scrub off the fungus (bacteria) with the tooth brush, reapply the solution let it dry. Wash the tooth brush in a bleach solution and run through your dishwasher to sanitize it. Repeat this daily. You might want to do this twice a day for the first week. You should see the fungus disappear quickly. She if you can get her out in some natural sunlight as well as that will speed the healing. Take the hospital tank outside with you while you do yard work. I'd wait a few weeks after it looks like it is gone before I put her back in the clean tank with the new substrate.

You need to look at how the bacteria or fungus got into the substrate. Was it kept too wet? Does it need to be changed more frequently? If you have any sand in with the substrate that can scratch the shell and let bacteria or fungus get in foot hold on growth in the shell. So make sure no sand is in your mix. If you can post a pickture of the setup I'm sure people can give you ideas for improving it to make your turtle happier and keep it healthy.

Let us know how she does. I dealt with a similar situation this winter with a Florida box that I got as a rescue. She is going fine now.

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