I had a GSP puffer that had some white marks on is side. It kind of looked like his skin was peeling way, or that he streched out so much that the green skin stared to seperate. I always figured it was dude to him getting scared and scraping simself on a rock. I had two in there so I kept an eye to see if both got it, but only the one ever had the large white spots. After adding some salt and montering for about a month everything seemed to grow back and be fine.
Not sure if this is what is happening with yours.
Again Pics would be helpful.