This is just an FYI that I noticed with the 2.0.4.1_experimental_2018-11-08 Docker container (in my case running Duplicati 2.0.4.2 experimental) any extra folders in the Destination for a job caused the error below.
This error did not happen with the previous 2.0.3.14_canary_2018-11-08 or subsequent 2.0.4.2_experimental_2018-11-12 containers.
Happy backing-up! 
System.IO.FileNotFoundException: Could not find file '/backups/_MyCustomSubfolder'.
File name: '/backups/_MyCustomSubfolder'
at Duplicati.Library.Main.BackendManager.List () [0x00049] in <365e0052627a43cbb8447250519b5a7f>:0
at Duplicati.Library.Main.Operation.FilelistProcessor.RemoteListAnalysis (Duplicati.Library.Main.BackendManager backend, Duplicati.Library.Main.Options options, Duplicati.Library.Main.Database.LocalDatabase database, Duplicati.Library.Main.IBackendWriter log, System.String protectedfile) [0x0000d] in <365e0052627a43cbb8447250519b5a7f>:0
at Duplicati.Library.Main.Operation.FilelistProcessor.VerifyRemoteList (Duplicati.Library.Main.BackendManager backend, Duplicati.Library.Main.Options options, Duplicati.Library.Main.Database.LocalDatabase database, Duplicati.Library.Main.IBackendWriter log, System.String protectedfile) [0x00000] in <365e0052627a43cbb8447250519b5a7f>:0
at Duplicati.Library.Main.Operation.BackupHandler.PreBackupVerify (Duplicati.Library.Main.BackendManager backend, System.String protectedfile) [0x0010d] in <365e0052627a43cbb8447250519b5a7f>:0
at Duplicati.Library.Main.Operation.BackupHandler+<RunAsync>d__19.MoveNext () [0x01028] in <365e0052627a43cbb8447250519b5a7f>:0
--- End of stack trace from previous location where exception was thrown ---
at System.Runtime.ExceptionServices.ExceptionDispatchInfo.Throw () [0x0000c] in <a6f810169ec746eeb2789b925e2858c0>:0
at CoCoL.ChannelExtensions.WaitForTaskOrThrow (System.Threading.Tasks.Task task) [0x00050] in <6973ce2780de4b28aaa2c5ffc59993b1>:0
at Duplicati.Library.Main.Operation.BackupHandler.Run (System.String[] sources, Duplicati.Library.Utility.IFilter filter) [0x00008] in <365e0052627a43cbb8447250519b5a7f>:0
at Duplicati.Library.Main.Controller+<>c__DisplayClass13_0.<Backup>b__0 (Duplicati.Library.Main.BackupResults result) [0x00035] in <365e0052627a43cbb8447250519b5a7f>:0
at Duplicati.Library.Main.Controller.RunAction[T] (T result, System.String[]& paths, Duplicati.Library.Utility.IFilter& filter, System.Action`1[T] method) [0x00271] in <365e0052627a43cbb8447250519b5a7f>:0
at Duplicati.Library.Main.Controller.Backup (System.String[] inputsources, Duplicati.Library.Utility.IFilter filter) [0x00068] in <365e0052627a43cbb8447250519b5a7f>:0
at Duplicati.Server.Runner.Run (Duplicati.Server.Runner+IRunnerData data, System.Boolean fromQueue) [0x00307] in <6abd47b91a774213b482ed288fd091a2>:0