iTunes and iPhone 6s plus do not sync properly.

I upgraded to a new iPhone 6s+ yesterday. Everything went smooth until I found out Music app has whole lists of library from iTunes although I only checked a few number of songs to be transferred from iTunes. All the music from 'my music' are playable. The weird thing is on Setting>General>Music, I only see the checked songs that I wanted. I resetted all content & settings a couple of times and spent whole night to figure out but still got the same result. I set up as a new phone. I tried 'recovery mode' to upgrade iPhone OS again but didn't work either. I am going to bring my Mac and iPhone to Genius soon. anyone has the same issues?