2009 Subaru Forester Secondary Air Pump problem

I just had a brand new engine and turbo charger put into my car. The engine is new from Subaru. The cost for everything was $8500. I got it home and after 3 trips to and from work the check engine light came on as I headed home. I have driven 56 miles on the new engine with no highway miles at all.
They read the codes and said that it is a secondary air pump issue but they haven't had a chance to get in and figure out why yet.
Is this something that should have been dealt with while replacing the engine or was it caused by replacing the engine? From all I see, it is not a cheap fix and I cannot believe I would pay that much for a new engine and turbo only to get back a car that sounds like crap and won't be able to pass emissions.