It’s happening in the purchased items sync phase when I connect my iPhone to my iTunes (step 4 of 8).
I did several things can’t guarantee what but two things worked on two different repeating duplicate files:
First: Make sure you have your files backed up using Time Machine on your Mac. Then make sure you have previously backed up a copy of your Device under iTunes - Preferences- Device while the phone is plugged in.
Went to iTunes preferences with -parental-turn iTunes Store to unclick- go to store-and unclick everything in all check boxes-OK
go to sharing, unclick everything there.OK
Go to Devices and clicked Prevent all iPods etc.. from syncing automatically. OK
Go to menu bar- Store-Turn iTunes Match and Genius OFF.
Turned off Wifi on Macbook.
In settings, turned off iCloud on my iPhone
In settings, turned off Find my phone under iCloud in Settings.
Plugged in iPhone to laptop.
When your device shows up in side bar click on it. go to Summary-Options-unclick Sync over WiFi-
click Manually manage music and videos
in your iTunes,
Take your original file (A) and your duplicate (A1)and drag all songs from the A1 into A. Hit Skip when prompted, Then delete file A1. Rename the file into something totally new. (for now)
Don’t worry all these are backed up in iTunes.
Go to Music up top and while, unclick your A1 files , do a manual Sync.
On the sidebar of iTunes click iPhone under ‘Devices’ Click arrow to open up a sub menu of whats on your device. See if there’s any duplicate files there. INCLUDING the original. Try to right click on the playlist under iPhone and duplicate playlists by right clicking. It either said Delete option for me or it said Export only. Depending on where I was at the beginning, during or after the manual sync did it open the Delete option for me. This was key. Kept trying it. Kept deleting all playlists that showed up in both side bars during manual sync on Device playlist opened and in my iTunes play list during sync. The new playlist was Renamed so don’t delete that. Eventually after a few manual syncs, the files started disappearing. So when they are all gone, go to iTunes preferences- Devices, click on your phone and Delete Backups. this stops the tainted backup from repeating. Make sure Wifi is off. Now eject your iPhone and plug back in, Click on iPhone on left side of iTunes and go to Summary. Click Back up now. Check and make sure theres no duplicates in both iTunes or in your iPhone’s playlists by clicking the arrow next to iPhone.
After back up, you should be in the clear to reopen iTunes store, turn on Wifi, and all your regular settings. But I’d still stay away from Clouds and iTunes Match but that’s just me. After you are free to go back to your regular settings, you can keep or rename your Renamed file to the same or not. Good luck. May not work for everyone but it worked for me. I’m running 10.6.8 on a MacBook Pro and iTunes 11.4. Simpler times before Apple ruined iTunes!