I have an iPhone 4S, an iPad2 and a new 15"MacBook Pro (the non-Retina mid 2012 version). I use iOS 6 on the Pad and Mountain Lion (with all the updates) on the MacBook.
I have pages, Numbers and Keynote installed on the iPad and MacBook, not the iPhone. But I (of course) use iCloud on all three devices to synchonise Contacts, Calender and Mail.
So far I have been very happy with the shole setup (apart from the fact that the iOS and OSX versions of the iWork apps have only a limited 'overlap' in functionality but that's another issue than the current one).
I have so far mostly (but not exclusovely) used iCloud for the iPad versions of a few documents and spreadsheets. But this morning I made a small Pages file and as I wanted to show it to a co-worker and was not going to take the MacBook along, I saved it in iCloud instead of in a documents folder. When I opened Pages on the iPad, there was only the new document, nothing else. Then - curious - I opened Numbers, only to see all my numbers documents for about a second and then they all disappeared.....
When I looked in the 'mobile documents' folder (in Finder, on the MacBook), there is also only that one (new) file.
And of course nothing in time machine, as 'Mobile Documents' is only a 'mirror' of iCloud, not an actual folder.
What do you mean with 'ghost files'?
And you are saying that your 'lost' files miraculously reappeared after 8 months or so?