Was the finishing of the garage and the installation of any wiring/plumbing etc. completed after the issuance of a building permit and was it inspected and approved by the proper authorities? Is the garage area finished (floors, walls, ceiling, trim, HVAC, etc.) using the same quality of materials and workmanship as the balance of the dwelling? Is the flow of the house and access to the garage seamless, or does it feel more like one is going into a former garage area that is accessed down a back entry/hallway?
Not that these questions are all inclusive, but they are just some of the things an appraiser would need to consider as to whether the former garage is included in your homes GLA. The majority of the time this is not the appraiser's independent call, but is based on criteria required by the lender/client. That said even though the garage area was not included in the GLA its value maybe listed on page 2, and it could be shown in several areas. You may have been given value for having an attached two car garage on one line and then additional value was given for the finish in the garage on another. Now the $64,000 question, did the appraiser deduct any value in the report for your not having a usable area for car storage garage while one or more of the comparables may have included a traditional garage?
Without seeing your home and the interior and without seeing the report it is tough to give you more specific answers.