Definitely covered. The civics are prone to fade on the roof, trunk,fenders, hood, pillars, and quarter panels. I'd go to your local dealer they should straighten it out for you. Just be sure to ask the procedure they do to fix it.
I've had to repair many of these in a body shop I used to work at. We had a big account with Honda and the blacks and blues would always have these problems. It's a paint defect from the company. The way it worked with Honda I believe is, no matter the year of the car you just go to the dealer...