That's definitely tire rub. That frame has horizontal drop-outs to allow you to adjust the forward-back position of the wheel. When you take the wheel out, look in the dropout and you should see screws in there. I found a photo on the slowtwitch forum. Back them out a bit and then do another test fit. Make sure that the skewer is properly tightened too so that the wheel doesn't slip forward under load.
As far as the existing damage, I would recommend getting a reputable local bike shop to take a look at it because it's very hard to tell just from the photos, but it LOOKS like the damage is just to the paint and possibly the superficial outer layer of carbon. Again, get an LBS to inspect it to be safe. If it's just cosmetic as I suspect, you can seal it with a clear coat of some kind. Clear nail polish works surprisingly well.