Macworld has a good article on Apple ID and issues users face around it. Majority of the issues mentioned in this article revolve around managing multiple Apple IDs and I have personal experience with issues revolving around managing two Apple IDs myself. I like most of the users started off with one Apple ID and eventually got my wife an iPhone and a Macbook Pro and had to get her own Apple ID to back up her iDevices independently. But we still use my Apple ID for purchases on the App store and the iTunes store. Though this setup works fine now, it took us awhile to figure this situation out and Apple does not make this solution clear.
Though Apple can be give the benefit of doubt in this situation as iCloud and Apple web services are (relatively) in their infancy, Apple has been getting a lot of flak about the unreliable functioning of its web services and with growing number of people who join the iOS family daily, Apple better fix this mess before it blows off into a full fledged disaster like the Apple Maps disaster.
I have to mention that Apple's iCloud works seamlessly most of the times, while backing up iOS devices or while syncing music through iTunes Match.