delerships, in particular their service departments, are hit or miss all across the country. Haven't used the toyota dealership here, but for Honda the dealer has maybe 5 different service managers, one or two are very good, but the rest can be outright maddening to deal with. It's all a matter of ferreting out the good ones.
Why the shop was relying on a local dealer to supply parts is beyond me - however, if you are having an issue, esp. if they are lying, go to SOA immediately and they will straighten it out. You could probably source the parts yourself from one of the myriad of dealerships who sell parts online much more quickly.
In any event, unless you are spending the $ on a premium nameplate where you are essentially paying extra to get the level of service you want, you never know what you are going to get.