The fact that there are two different numbers means that two different applications are being referred to. One can be built, the other cannot.
The "Grant Certificate of Exemption" sounds like it is a reference to a Certificate of Exemption from Planning - i.e. either the owner or the architect was a little worried that the extension might not be in compliance with the exemption (40 sq m. etc. etc.) or wanted to make sure that all their paperwork had the i's dotted and t's crossed.
I don't know this for certain, as I haven't seen this particular reference on a Planning Website before - but I can't imagine it is anything else.
At a later (or earlier) date the same owner applied for permission for an extension which required permission (because of its size) which was refused.