Ran into this issue a couple of times myself. I was able to determine that the meta data in the MP3's were causing the issue.
How I fixed it, was to use
MP3Tag, and Windows Media Player to rewrite the meta data.
This was for MP3's only!!! As I don't have any other formats.
First I used MP3Tag to update as much of my meta data on my files as accurately as possible on my computer. Then used Windows Media Player, Tools, Options, Library, "Automatic media information updates for files, Retrieve additional information from the Internet, Overwrite all media information" selected. Then let it go do it's thing (it may take several hours).
I then deleted all the MP3's off my phone, then copied things back from my computer to the phone. This fixed two issues, "sorry, we cannot play this file on your phone", and duplication.
Now, I do recommend that you backup your music collection before letting Windows Media Player do it's thing, as you may not like the new meta data it puts in. You can always go back, with the backups.