I had a similar thing happen to me a few years ago, I bought a Colnago off ebay and when I recieved it the wheel axel had scratched the paint off the frame the size of a quarter. The guy I bought it from was very fair and offered to give me $200 back on the bike, I ended up spliting the difference with him and used fingernail polish to cover the paint. The fingernail polish did a pretty good job of covering it up, bike still rides great and you can't even tell from 5 feet or so away.
Guess this is a common bike packing mistake.