Thanks for the comments.
I received a phone call from the Nationality Checking Service this afternoon. They are looking into what happened as I should not have received that letter...
I an waiting for them to get back to me but in the meantime I have also sent a letter to the Home Office.

Hello, I submitted my application for British Citizenship on 06.11.2015. It was done at the local Nationality Checking Service. They assured me that the residental qualifying period would be worked out from the day THEY recieved my application (6th November). Having returned from my holiday a letter...