I've been having the same problem with mine. He had one tiny spot and it multiplied. I took him out of his normal tank on sunday. Washed him with a tooth brush, put him into a container with warm saline water. Let him soak for 20 mintues and let him completely dry off. I investigated the spots again and they weren't soft, and I couldn't peel anything off. I kept him out of water for about 6 hours under a heat lamp. (like he normally does his basking) Put clean water into another tank for the night. I've been doing this everyday since sunday. The spots are now not noticeable when he is dry and when you look down on him from the top. I thought it was maybe shell rot, but the spots are tiny and random. Different from the pictures I have seen of shell rot. He basks regularly and his water is clean. I don't understand either, but keeping him super clean seems to be helping. Good luck