So I bought a used forest green, 2002.

Hi, so I bought a used forest green, 2002 toyota highlander 3-4 months ago from the dealership. It runs well, the interior is extremely well kept, as with the exterior. I've had to replace a couple items but for the most part it's in amazing condition for its age. The car shines perfectly and ever since I've bought it, I've washed it once a week. When I wash it, I use a common car wash soap mixed with water, and scrub it down, then I dry it; however, I've never scrubbed down the roof because I'm too short. So I just spray it with soap, wash it down, and let it air dry. After a couple nights of a really heavy rain storm, I noticed a spot, around 6x6 inches where clear plastic, or paint, was peeled off and the edges are peeling. One of the pictures shows this. Also, the rest of the roof is filled with these small circles that look dirty but aren't peeling. Again, theres 2 pictures for that. The whole rest of the car shines perfectly, with mild scratches from the previous owner. I've read that this might be clear coat failure, but it doesn't really look that intense, if anything its extremely mild and is only on my roof. Anyone want to tell me what this is, how to fix it, and if so how much it would cost? Someone told me to wax it to add a layer of protection or to spray a clear coat on it. Help!