paint problems

Hello Everyone, Apologies if this is a common issue, but I was unable to find any threads about it when searching. I have a '21 CTR in Sonic Grey Pearl and recently I noticed some brown "spots" on the roof. These spots look almost like rust or like the paint has been stripped, but to the touch...

In a phrase: not good. So a few months ago I picked up a 2017 Civic Touring sedan as I needed a vehicle to commute approximately ~50 miles each way a day to work. I ended up getting a great deal on the car, but after driving with the car I'm starting to wonder if there was a reason for it...