advice needed carbon frame

the ferry

i've just noticed my rear wheel in my trek madone has rubbed the laquer off one chain stay, the frame seems correct when i've checked the alignment though the rear wheel takes some fiddling to get it to sit right. that's the case for the bontrager racelite and the 105's.
is it real bad news having the carbon exposed?
why would a wheel not be centered correctly?
thanks for any suggestions.