When your attorney receives the contract for you to sign, they should also ask to see the Certificate of Occupancy. This will tell you how many floors the house has. If the seller has finished the second floor (or a previous owner did), the CofO will be dated after the completion of the house. You should not sign a contract until this is resolved. The mortgage lender is going to want the title company to insure the title of the house, but they will only do so if everything is legal.
As an appraiser I come across this all the time with capes. In an older cape this sometimes occurs because when the original plans were submitted to the county the second floor was not finished and considered an unfinished attic which is not counted in the gross living area(gla). Or the current owners may have measured the home themselves and done so incorrectly. Or the current owners may have refinanced the property and taken the gla from the appraisal. Below grade area's (basements) are not counted in gla. You should make your concerns known to your attorney. He/she will ask the title company to be involved and will try to resolve the difference. If it cannot be resolved early then you will have to wait until your bank has the appraisal done and there is a gla based on an actual recent measurement. But don't be surprised if you get a 3rd number! Capes are funny that way. I would also check to see if there are any open permits or additions to the property which were made without a permit. This would mean that a part of the home has no certificate of occupancy for any additional work done. The C of O protects you from work that may have been done that doesn't meet code. It means that inspections have been done by the proper authorities. Speak to your attorney. Good luck.