I've noticed a few times when I made a first backup that the file size is only a few KB or MB's. Obviously the backup is not made completely while is says it's completed. When I make new manual backups it works at some point but takes some extra time. Also, I'm a bit worried the Hub is giving wrong info and I need to be sure the backups are done perfectly. I'd love to use this update/backup system for all my sites.
I hope there's something you can do about it and ensure backups are done properly in the future.