Don't bother going back, it won't be worth it to get a refund. The bike technically is OK it's just a stupid mechanic and assembling. Pedals are not included in the price of a bike, so really you would only get a refund on the installation costs and I don't imagine that would be huge.
Find another bike shop, ask what training do the mechanics go through (Shimano does a training course, so does Specialized) and see their certificates. Ask other cyclists for store reccommendations.
I know of one lady whose crank was mis-installed and on a sprint her whole crank arm came off attached to her shoe. Lucky she had just started the sprint so she was able to stop safety. She had only had the bike 3 days.
The bike wasn't damaged so we all told her "find someone else to look after it and never go back to that store unless it's under new ownership".
If you are really still angry about this write to Trek advising them about the poor service from this shop for their product. They won't like that their brand is being mis-handled and probably will talk to them.