I would not assume that the manufacturer builds the bike all the way up to rideable, then disassembles it minimally to put it in a box, unless it's being sold direct to consumers. So, yes, it is up to the SHOP to assemble the bike, set up and adjust the brakes and shifting, and make sure every fastener is properly torqued down.
And, you know, the best shops make the occasional error. And to claim they've built thousands of bikes and never made such an error? How in hell would you even know that? Did you ask their thousands of customers? Ever think that maybe the rare mistake got handled like yours, with the shop fixing it for free and sending you back on your way?