Roof flashing under new shingles?

this is the right way to do it ... flashing goes under the shingles

Well, this is what happens when you don't look at your work in detail and write down the specifics of what you expect. It will last long enough for the roofer.  Who knows if it will last long enough for you.  Nowadays, you see lots of pressure from insurance companies for roofers to reuse existing materials instead of replacing with new materials.   This sounds like that kind of situation. It is the way the insurance company does it.  S. Farm?

Hopefully he used roofing cement (tar) under the shingles that cover the flashing. Was this another layer of shingles?? If so, it shouldn't be a problem if it wasn't a problem before.