I had a similar winkle on the top tube on my 2100. I believe it came when I had the bike in the repair stand. I decided to leave it be. My only suggestion would be to gently heat the decal with a hair dryer and try to smooth it out with your finger.
I bet a Trek dealer could get replacement decals for you, but sometimes they are covered with clear coat and it may be a bigger deal to change it than what you may want.
You could also bring it to the LBS that mounted the accessory and see if they can help.
I know how you feel - I try to keep my bike perfect, but with 3,500 miles on it since last June, the little dings are starting to add up. I guess it's part of the game.