I suspect concurrently updating and deleting the same document by query might cause this. As far as I know both operations work based on a snapshot of the data as it was when the operation started, so if the operations take a long time and affect a large number of documents it is likely that version conflicts may be detected if multiple operations affect the same documents.
There seem to be a parameter determining how conflicts are handled, have you used this? If that does not help, have you considered altering the size of the update and delete requests?