Does the enclosure have a dry out area as well as wet/moist/humid? Those little white patches appear in this pic to be the onset of bacterial/shell rot.....I would suggest that you assure there is a dry out area in the enclosure....I also would use a soft bristle tooth brush, soak the tort for a bit, gently rub the toothbrush over the area....you can use a topical athletes foot cream on those patches for a week or so (see how the spots are responding) and see what all looks like then. It is important for a tortoise to be able to dry their shell out so the shell remains healthy....
The spots seem to be gone this morning. I still applied more cream. I know that bacteria and fungi go through cycles and seem to disappear but are actually dormant.