If it's a repuatable shop they should replace at mimimum the frame.
I had similiar issues at the end of 2010 when I bought a brand new Scott CR1. Looked it over at the shop, took if for a short spin from the shop after saddle adjustment etc. Everything seemed fine.
When I was removing the bike from my truck when I got home I noticed several chips in the head tube..Paint only. I took photos and emailed them to the shop after speaking with them over the phone. This shop is a 2 hr drive for me.
Bottom line is they are an awesome shop. After emailling the pics, they called me and told me to ride the current bike untill they had a new one in. At that time, they swapped groupset and tires that I had continued to ride onto the new frame. They apologized for letting it go out that way and we both understood that these things happen. I would buy from them again in a heartbeat.
Hope you have the same response from your lbs.