Appraisers are busting deals right and left here in Texas. The problem with the difference in square footage is that they don't usually go in and measure the other houses that they are using as comps so it is not "apples to apples"; they use the listed square footage on the comps and their measured square footage on the subject property so any adjustments they make are always going to be questionable but not changeable. Additionally, they go back too far in quickly appreciating markets rather than look at other similar neighborhoods for more recent sales and that often brings down appraisal values as well. Sadly, while market value in it's simplest form is "what the market will bear", appraisers have a lot more rules and are held to a more conservative standard because at the end of the day, their job is to protect lenders from ending up with over-leveraged houses when buyers default. They are not held to any accountability in the transaction as they have no skin in the game and they are considered the expert regardless of the numbers so sadly, it's very difficult to get around a bad appraisal. If you care enough to maintain a record of these low appraisals and then go back and see what the homes actually sold for, maybe a body of evidence large enough to make a change could be collected but I doubt anyone in this industry has the time to do that!