Some of the files were not copied to the iPhone because iCloud Music Library is enabled on this iPhone. So you need to turn off the iCloud Music Library before syncing the files to iPhone with iTunes. After turning it off, you will be able to sync your desired files without any hitch.
Step 1: On your iPhone, navigate to the "Settings" menu and then, scroll down to open the "Music".
Step 2: After that, disable the "iTunes Music Library" option and then, again try to sync the iTunes files to iPhone.
