I'm having the same problem. I just dragged and dropped two albums over from my MacBookPro to my iPhone via the Music app. One of the albums actually shows on the phone. The other does not, but both are indeed showing in the Music app on the MacBookPro when I click on the phone!
I searched by song on the phone itself -- nope.
And this is one of MANY, MANY REASONS I still rely on my iPod Classic for portable listening. The phone absolutely sucks for music and podcasts.
In this example, the two albums are the mono and stereo versions of the U.S. version of The Beatles'
Help! album, both of which were not previously on my phone. I dragged both to the phone. (I use the "manually manage" option; the "sync" option NEVER WORKS the way I need it to!)
The stereo album copied over. The mono album did not.
As you see, in the MBP Music app when I click on my phone (named "Stephen" -- that's the phone's name, not MY name! Long story, but I have a Weber Grill theme going on with my Apple devices), it's showing that both copied over. Ooooooooh, I beg to differ.
When I search my phone for the word "tyrol," two songs should pop up: "In the Tyrol (instrumental) [mono]" and "In the Tyrol (instrumental) [stereo]." Only one appears.
I rebooted the phone, nope. The songs claiming to be transferred didn't appear but still showed up on the computer end. Deleted and tried again. Same thing.