As a shop owner with 30 years experience here are my comments. There's missing information. Did the old pedals have to be removed before installing the new ones (Keep in mind it takes a special tool to do the job and was it a TruVativ crankset)? Was other work suspended to do the job and was a stand available or did they have to wrestle the bike? Did you pay full mark up on the pedals or were they on sale or discounted? In days past when shops were able to charge MSRP there was some margin for free installations without losing money. The job cost much less than than the price of the special tool (Which could be a pedal wrench or a 6 or 8 mm hex wrench, and don't forget lubing the threads).
Was the bolt "you" broke on the rack or was it broken off on the frame? Small 4mm or 5mm broken bolts can be very difficult to remove (Easy Out type tools only work well on larger bolts and other methods like Dremeling a groove or drilling are dicey) and a bunch of the time was probably spent trying not to damage the rack or frame. Did you drop off the rack/frame so the job could be slotted into the workload or did you wait around so everyone had to stop what they were doing to try and help you out? Sometimes you fail and have to refer the customers to a machine shop, but you tried to fix "their" mistake and save them money, so the attempt is worth something. At the very least you should have beat them to punch and offered the shop something for their effort.
Regardless, all this only cost you $15 - $18, and I guarantee you it cost the shop more than that. In my experience, shops do try their best to provide great service & reasonable prices and promote good will, especially for steady customers, but it works both ways. In this case you owe the shop at least a 12-pack of micro beer for thinking badly of them. And I'll bet they won't charge you for a small job next time