I've been using Ubuntu One for a few days and I think I've found my beef with the service: conflicts. Conflicts are unavoidable in a scheme like this: you dump documents into it using one computer, then from another computer you modify those documents. In the process of syncing back and forth, you're going to run into a situation where you have updates on either end. Which one should take precedence?
It would be nice if in these situations Ubuntu One at least asked what it should do, but what it simply does is to rename the directory by adding the words "conflict" to the name. What actually happened here? Which version was followed? Well, I'm not sure. The documentation is a little sparse on that, too.
Quite possibly the only mention I've seen on conflicts is a post on the Ubuntu forums, but that seems to have gone unanswered. So which is it?
In the meantime, I would probably recommend just using Ubuntu One for offline backup, not as the main storage area. Files should probably be compressed and saved with different version names.