WHEN TO APPLY
(This is in Tier 1 (G) Section)
http://www.ukba.homeoffice.gov.uk/visas ... -to-apply/
So, in order to avoid an extra extension, you can apply within last one month of your permitted stay.
And in fact if you're late, you can still apply within 28 days after your visa has expired, but I am not sure about any other consequences related with it.
your initial visa expiry date is 15 Nov so you should have applied for extension between 16 Oct to 15 Nov.
But again, it all depends on the case worker. In your case, he/she should have given you extension from 15 November. Cruel decision. Ideally you should have raise this issue with them in the public enquiry office.
If I put myself in your shoes, I will write them immediately and will give them the above link explaining that I was in impression that I could apply between 15 Oct and 15 Nov in order to get extension from expiry date of previous leave instead from date of appointment. I think they will sort this out for you. They should!
Even if they do not agree, I don't think you will have to apply for an extra extension. Just apply for ILR
by post during last week of your current leave and you will be fine.
Also you arrived in the UK within valid 90 days, so that's not an issue later for your ILR.