Depends on the roofing company. Some like exposed metal some like to cover it with a layer of shingles. The shingles would be under the apron metal but they install another course to cover the metal. Why would you call out a face nail if it's caulked. How else do you nail down the leading edge of the metal. As long as they are caulked it's not a problem. There are many areas that are faced nailed like a top of hip or the finish tab on the ridge. Just gluing the shingle down is not efficient. Eventually the sealant will fail and the shingle blow off.

The corner of the chimeny is wrong though. The step flashing should be on top of the notched shingle. In this instance the application of the apron and first piece of step flashing is wrong and should be corrected. If you look at the corners the water will run down the side and under the shingle from what I can see.