In iTunes 12.5.4 I have found a potential solution to this problem...
Do not remove songs from your device... use only the computer that iTunes is loaded on.
I experienced this problem this morning (1/13/2017) and found it only duplicated playlists when I edited the list on my device (in my case an iPhone 6s).
I deleted a song I hated from my phone.
I have my phone set to update when on WiFi, so it pushed the change to iTunes... and duplicated the playlist...
I then found the "updated and duplicated" playlist in iTunes...
The playlist 'iPhone songs1' contained the song I deleted but the 'iPhone songs' playlist did not.
I then went into the settings for updating and removed the checkmark from the 'iPhone songs1' list and went back to iTunes and deleted that playlist.
This now makes me wonder...
If any changes are made on the device, the device then updates those changes to the playlist and then renames the old one to xxxxx1, xxxxx2, etc.
I know this won't stop the duplication... but I hope it helps someone figure out which is which or help in some way.