I'm having the same problem here!!! I just purchased Lenka's new album (didn't even know I was purchasing an LP album, but oh well) -- DOUBLE SONGS, minus the music videos. The music videos aren't duplicated.
I tried erasing the songs on my iPhone 5 -- it worked, BUT THE LENKA ALBUM WAS STILL THERE!!! Remember -- I had NOT been using iTunes Match on my iPhone since I realised it drained the battery (downloading the music)! All these problems only started happening (at least with me) with iTunes 11!! I see that it goes past that, but nevertheless, I think it's an iTunes problem ... iTunes and the cloud.
So yeah, all my music is now gone -- sans the Lenka album, and guess what -- I CAN'T PLAY THE MUSIC IN THAT ALBUM. They are all greyed-out. It's as if iCloud is saying "Hey, you got this nyeh nyeh, but you don't have an internet connection to download it" HUH?? Or it's also what you get if you interrupted SYNCING, such as what I did when trying to resync the iPhone. Later on I completed the sync and now I have my music back..
... AS WELL AS THE GREYED-OUT DUPLICATES.
Granted, the duplicates don't play, and they don't seem to take up any space. 3MB of space, that's all. For ten songs?? That don't play??
APPLE NEEDS TO FIX THIS!!!
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UPDATE: The fix above works!!! WOOHOO~!! THANKS A BILLION! What I did was go to the artist (Lenka) and because I have songs from two of her albums, I just deleted the album (by swiping it on the iPhone 5) that contained duplicates (TWO). Then a re-sync with my macbook pro put it back, without duplicates!