This happens. It's a matter of consistency. Sometimes in a visa office or a processing centre, this is very common. The officer would finish his job and on an operations side would not put the exact information into the system. The letter or the work permit, or whatever the extension was, was sent to the client. However the call centre could not see it.
I'm not privy to the details of how the system works. However, this happens from time to time, and I can tell you that the GCMS, the system that is used right now, is the best system to get this result, because it is instant. When you make a change, it automatically affects all individuals who see the file. It's human error these days; before it used to happen very often.