That is a unique situation. Appraisals are based on appraisers opinion of value & supported by recent sales. From experience 2 structures on one deed is difficult to find. Typically the recent sales must be in the same general geographic area as the property being apprasied must have sold in the last 12 months (some lenders will request 3-6 months max) must be of similar general amenities. With a small residential income property the value is also driven by the income potential. The income as compared to other sales & the value based on recent sales should be close to help support the total opinion of value. That being said... Sometimes due to market conditions & unquie properties finding truly comparable recent sales can be very difficult. The appraiser is left to either expand he geographic search, or look for similar but not perfect recent sales to complete the assignment.
The issue could be 1 of a few things.
1) The lenders instructions (assuming there is one) didn't allow the appraiser to extend the geographic search enough to allow for enough recent sales. Keep in mind that if there is a lender even if you paid for the appraisal the client is the lender & the appraiser must follow thier instructions.
2) No recent sales similar to your property sold in your area in the last year.
3) The appraiser missed something. I know great ones & not so great ones and human error is possible. If you know of any recent sales similar (2 homes 1 deed) tell the appraiser about them. Pull the deed, take a picture, give them some tangible data that shows they were in deed similar in size, location, amenities, etc.
Appraisers often feel the value on thier report could have been higher or lower then the reported value, however thier opinion must be supported by factual data. A lack of data can fluctuate value opinions until a sufficient number of similar properties have sold in the market place.