I've been experimenting. I'm sure iTunes is the cause of most of my issues.
Adding albums to My Music via iTunes seems to frequently miss tracks, or set tracks as unplayable. Even though these tracks are playable and visibile when you preview the album on Apple Music before adding to My Music.
Adding albums to My Music via the app on iOS seems to be far more successful. It will at least display correctly on iOS, however viewing that same album in My Music on iTunes will be borked frequently. I can live with that for now as I use my iPad/iPhone more.
To fix the issues with missing tracks that I've had so far, I've removed the album from My Music (on iOS) and let that replicate through all devices and to iTunes. It's pretty instant. I've also made sure to remove from downloads on iOS before removing from My Music. Once it is gone, I search for the album on Apple Music via iOS, making sure to show the complete album if some tracks are hidden, then add to My Music. Seems to add the full album. Again, if it was borked before on iTunes it probably still will be, but at least its fine on my devices.
This won't help with the bad matches when trying to add missing albums from your collection, like a Live album, where I often end up with a poor match to a studio album. But it does at least solve the missing tracks for albums that are on Apple Music already.