Hi
I had the same issue with some songs but have managed to fix I had some music which was missing whilst other music was there (even on the same album)
If you have iCloud Music Library enabled it is worth looking at the bitrates of the files. I think they have now enforced minimum bit rates if iCloud music is switched on- iCloud music uploads seem to work the same way as iTunes Match - i.e. it will not import files which are below a certain bit rate http://www.macworld.com/article/1163676/secrets_of_itunes_match.html.The ones which weren't uploading were all under 80kbps (either MP3 or AAC, inc variable bitrates).
In order to solve this I started with both iTunes music library enabled in iTunes 12.2 and on the iPhone settings.
1. sorted the files by bitrate in iTunes 12.2 on mac
2. selected anything below 80 kbps then right click > convert to AAC (I use the iTunes Plus conversion setting).
3. iTunes will then start chugging away uploading the new version to iCloud...
4. once all converted - backed up the low bitrate versions and then deleted them from iTunes 12.2
Don't get me wrong this was a pain as the new version had to be added to my manually created playlists again...
Note - after a little point the songs will start showing up in your searches on 'my music' on the iPhone - however they may not be 'your version' of the song - i.e. they are what Apple Music has selected ... (I don't have iTunes match so I am assuming that is why that is happening...)