Yea, it's not something we can fix. We kind of skirted around the problem with the website version previously because technically we could access the files directly on the file system. We could do the same with iCloud Drive, but in the last (nearly) 2 years of working with iCloud Document Syncing (now iCloud Drive) it never really worked as well as it should've. For some it worked great, for others it was constantly prone to problems.
So, we switched to CloudKit syncing, only available in iOS 8 and Yosemite. This, however, does require that you have MAS and App Store versions of each application as CloudKit is more or less a database in the cloud. To access all of that does require the Mac App Store version. On the plus side, this means we get real errors that we can use to troubleshoot issues with users experiencing problems and removes a great deal of guesswork. It's also incredibly cool how it all works. It's the iCloud sync we kind of wish we had from the beginning.
We included iCloud sync in the website version because we could but we never really advertised that because it could disappear any day.
Wifi sync got some great updates though, it's now automatic, can sync all vaults and includes attachments now

It's almost enough to get me to consider using it full time now and probably will once I get my Mac Mini setup after moving and use it as the master computer for all syncing.
If you were adversely hit by the iCloud sync issue, please let me know via private message so I can see what we can do to assist.