i'm limited in my ability to fully test at the moment. From what I've seen though is using iOS 8 and Yosemite with iCloud basically moves your iCloud files to a new location in iCloud that is only accessible to applications that target the new OS's.
What I assume they are doing is on first instance of trying to use the App, they are actually moving the files to a newer instances of iCloud that has features or some sort of abilities that the current now 2 year old version of iCloud doesn't support. This is just an assumption, but it makes sense that they are handling iCloud Documents and iCloud Drive slightly differently.
This is something that I'd imagine has more to do with something as trivial (though simplified in perspective) as looking at icloud.com (for current stable OS's) and beta.icloud.com (for iOS 8 and Yosemite).
i know for iOS 8 users there is a new version of Pages, Keynote, and Numbers that probably point to the new location. I'd imagine that for any iCloud Documents (current version of this) it will work fine with existing apps though.
For example, i don't have the new iWorks suite on my iPad Air so they don't seem to work at all. But PDFPen which hasn't been updated (quite frankly a piece of junk but syncs PDF's across devices) works fine.