I had that happen on my truck, but it was after about 4 years. Most definitely it was from wear. The paint they used was quite thin, I guess they wanted the numbers to illuminate but after awhile the most often touched areas wore down and the light would show through.
Yours is a bit different than my truck though. It's hard to tell if the paint is wearing off or not in the picture. In any case, in my truck, they just replaced the whole unit (6 disk in dash cd changer/mp3) and didnt bother with the buttons. I was surprised, but I guess under warranty, that's how they do things at Ford. It was a 30min process, so I can't complain. Although, it did start to happen again right before I traded it in earlier this year for my car.