Welcome to the Apple Community.
Try the following:
- Save the documents on the iPad that has the full versions on to iTunes.
- Turn off syncing of documents on all devices and restart them.
- Transfer the documents in iTunes to the desktop on your computer.
- Rename them so they have different names.
- Turn on syncing on all devices.
- Upload your renamed documents to iCloud.com
This exact same problem is happening for me, except with my music instead of documents and its on my iPhone 4S. I sync iTunes with iCloud on my Mac, some issues come up with duplicate copies and wrong metadata so I delete them all from iCloud and start fresh, and now when I turn on iTunes Match in Settings I have around ~180 ghost songs sitting in the Music app on my iPhone that cannot be played or deleted or anything. My Mac says there's nothing in the cloud, though.
There's something up with iCloud and files becoming corrupting during synchronization, or something. I'm at a complete loss for what to do just as you are. Its like the corruption isn't local, its on the cloud, and your device and your Apple ID keep pointing back to it as long as iCloud features are enabled. For what its worth, restoring did nothing to solve my problem.
I HAVE THE ANSWER!
Apologies for shouting but this is my solution:
1) Make sure the 'good' files are backed up first
2) As Winston said, turn off icloud in pages and icloud settings
3) As Winston said, reboot any devices
4) The solution . . . open Safari browser and sign in to icloud - the key here, is that I was previoulsy using Google Chrome as my browswer. I saw ALL my files there, included the ghost files that were not visible in Chrome. I deleted the lot, one by one. When I switched icloud back onto ipad and iphone all the ghosts were gone. iCloud is working on all three devices (PC included) and I have cancelled my Genius Bar appointment (hopefully not too early). I hope this saves others the day and night its taken me!!