I had that happen a few times as well. I think it was due to me stopping and starting iTunes Match several times. On my iPhone it was just as bad.
It to where I turned it off on my phone, downloaded the 256 songs on my computer, turned off match on the computer and then synced the songs to my phone. It still did some weird things.
I have Led Zeppelins Physical Graffiti on my phone. I have only one copy on their of course but it shows CD 1 two times and I can't get rid of it.