More iCloud Core Data synching woes
I was facing something similar with few uses ( by your description I assumed you have way more volume than I do, that's might the reason for several cases )
In my case Apple seemed to have removed without earlier notice the 20gb free space in the icloud. I noticed that the 2 uses who are power data usage users had lost of new data from my app (which was to deal with historical stock pricing ) and the others ones we just fine downloading the same data size.
I followed up with those 2, helping them to clean stuff up to let more space in icloud and voila, after downloading the data again it worked fine.