Tortoise shells are not supposed to flake or peel.
We'll need all the info about how you are housing your tortoise. Really any info will help. Where did you get the tortoise, how long have you had it, how was it cared for before you got it, etc...
I got it from petsmart a few months ago, housed as below, regular bathing and healthy diet, temps, and the ability to graze outdoors daily. Petsmart not being the best of choices, probably started some kind of bad healthy I'm trying to reverse.