Same thing. I deleted all of my matched & uploaded music within iTunes from both my Mac and iCloud, but no matter what I do I can't make the songs disappear from my iPhone Music app where they are still listed with cloud icons next to them, but not downloaded to the device. They're still pointing to their files in the cloud, which were deleted. I don't know what to do. Backup & restore, hard reset, toggle cloud and match features off and on, nothing works.
They don't come back in my iTunes library on my Mac no matter what I do, they just stay on my iPhone. Broken. Like ghost tracks that I can't get rid of. I brought my iPhone in to an Apple store to ask the genius bar about it and they were stumped, but told me its probably a bug on the service end and hooked me up with the support line to call tomorrow.
I'm not sure the exact steps you are using to delete items from the cloud, but here's what I do. First, I delete them from the library and opt to also delete from iTunes Match. I do this by highlighting the items to delete, hitting delete, and checking the box so they'll be deleted from the cloud (so not by option-clicking)
Then under the Store menu I select "update iTunes match." If you don't do that, it may be some time before a fresh copy of your library database is uploaded. Even then, I get the feeling the cloud database can take some time to update.
Finally, I confirm the database has been updated by looking for the album on my iPhone, iPad or AppleTV.
JiminMissouri is right, but when i had to do mine, I had to delete them a couple hundred at a time. After each time I deleted about 300 tracks or so and do an update iTunes match right after. Had to do that until they were all gone and started over. It's also a good idea to do this by creating a new iTunes library and adding it to connect to iCloud and that way, it won't get confused with your local tracks.
I just read something that may explin why chanwise needed to delete in groups. Someone who was working to delete an entire library found that you can't delete more than 1000 at a time. They also mentioned that it does take some time for the deletions to process, so if you deleted and quit iTunes or closed a laptop lid, you'd interrupt it.
Deleting around 8-900 songs at a time then updating match every time seems to have worked! The process:
Select under a thousand or so tracks. I tried to keep it under a thousand.
Every two or three deletions run an update iTunes match.
I didn't wait for the update to finish before deleting more tracks.
Keep iTunes open for a while after deleting. I just went to sleep, and my MBP went to sleep at some point.
If you have Little Snitch, turn on the network monitor and you'll see iTunes talking to one of the iTunes servers. This is what you want.
Finally, I can upload more stuff to iCloud.
Note that you can exclude tracks from iTunes match by changing them to Voice Memos. You won't get Album Art, but they still do show up on the Apple TV and the still show up in playlists.