I too realized this was happening for me, and read the iCloud features page more closely. Apparently, it doesn't actually do what we want it to (and what I thought it was presented as doing). It only automatically syncs documents across iOS devices, but not Macs. Lame.
This is the quote from the iCloud documents page :
"
iCloud makes it easy to move Pages, Keynote, and Numbers documents between your computer and your iOS devices. Just sign in to icloud.com/iwork in any modern web browser, and all your iWork for iOS documents will be there — complete with your most recent edits. Click a document to download it in iWork ’09, Microsoft Office, or PDF format. You can also drag and drop any iWork ’09 or Microsoft Office document from your computer into one of the iWork apps on icloud.com, and it automatically appears on all your iOS devices, ready for you to review, edit, or present.
"
So to sync with the Mac, you have to manually drag and drop into the iCloud interface.
I really hope Apple updates this so that it automatically syncs with Macs also, because otherwise it's usefulness is severely limited.