This stuff happens quite often. Through HS and college I worked at a ATV/snowmobile/motorcycle/Harley/JD dealership, a car dealership, and a marine dealership. The parts managers (or the owner for the marine shop because it was small) knew their parts inventory pretty well but there was always some stuff just thrown in by someone who didn’t care to take the time to put it away right or label it properly. Probably what happened here and Mr Murphy rode in on your shoulder and you got the unlucky part.
Personally I think they should have given you a new chain. Telling you to run it loose to burn the burs off is kind of bush league IMO.