Immediately after upgrading 6S iOS 10, songs in Apple Music (which are stored locally on the phone) appear to be duplicated In the app. however, If you look at storage/usage there is only one copy of the song locally. In some albums one copy of a song is greyed out ("item not available - this item cannot be played"), while in other albums you can click on either of the songs and they will play. Albums downloaded post-upgrade appear fine.
Browsing music library on Apple TV now shows the same issue.