Having the same issue here. Here is some stuff from the log where it happened:
cloudd(CloudKitDaemon)[135] <Info>: Checking TCC authorization for bundleID:<private> with 1 proxy
cloudd(CloudKitDaemon)[135] <Info>: TCC accepted a token for bundleID:<private>, proxy:<private>
cloudd(CloudKitDaemon)[135] <Error>: Error getting CloudKit auth token: <private>
cloudd(CloudKitDaemon)[135] <Error>: Finishing request with error 0x17dafe80
cloudd(CloudKitDaemon)[135] <Error>: Error fetching database URL from the server: <private>
cloudd(CloudKitDaemon)[135] <Info>: req: <private>, "<private>, did finish request <private> with error <private>"
cloudd(CloudKitDaemon)[135] <Notice>: [Operation 0x17d422e0] Operation is finishing on callback queue with an error
cloudd(CloudKitDaemon)[135] <Notice>: [Operation 0x17d422e0] Operation is getting flow controlled due to a local error
cloudd(CloudKitDaemon)[135] <Info>: Got an error from CKDContainerSpecificInfoOperation: <private>
cloudd(CloudKitDaemon)[135] <Info>: Finished operation <private> with error: <private>
cloudd(CloudKitDaemon)[135] <Error>: Finishing request with error 0x17dafe80
cloudd(CloudKitDaemon)[135] <Info>: Fetch records url request completed. Waiting for all record callbacks to finish before completing request <private>
cloudd(CloudKitDaemon)[135] <Notice>: [Operation 0x17ef8bb0] Request 0x0 set on operation
cloudd(CloudKitDaemon)[135] <Info>: req: <private>, "<private>, did finish request <private> with error <private>"
cloudd(CloudKitDaemon)[135] <Info>: All record callbacks are complete. Finishing request <private>
cloudd(CloudKitDaemon)[135] <Info>: Failed to fetch records for <private>: <private>
cloudd(CloudKitDaemon)[135] <Notice>: [Operation 0x17ef8bb0] Operation transitioning from state 2 (cancelled=0, stop=0, error=1)
cloudd(CloudKitDaemon)[135] <Notice>: [Operation 0x17ef8bb0] Operation is finishing on callback queue with an error
cloudd(CloudKitDaemon)[135] <Notice>: [Operation 0x17ef8bb0] Operation is getting flow controlled due to a local error
cloudd(CloudKitDaemon)[135] <Info>: Finished operation <private> with error: <private>
My log of the error:
<CKError 0x145eceb0: "Not Authenticated" (9/1002); "Account doesn't have access to CloudKit account">
This started on iOS 10.1 Beta.