Are you perhaps confusing the various URLs/paths in your setup?
You have the URL for your persistent store. This is usually a path in your sandbox somewhere (e.g. Application Support). You can store it in the ubiquity container with the nosync extension, which looks like what you are doing, but it is not necessary.
In addition to this, there is a second URL which is used by iCloud to store log files for the sync. It's basically a private folder. That is what the NSPersistentStoreUbiquitousContentURLKey setting is for.
Your persistent store should not be inside the log file folder. Make sure the two are separate.