You're not being punished. The underwriter is calculating the amount of income they can use for your approval based on the Adjusted Gross Income on your tax returns. When you have business expenses on your returns the underwriter has to subtract that from your income which reduces the amount of income the underwriter can use. In your case the underwriter is trying to determine if the business expenses in 2013 were a one time thing or if it will occur again. If it was a one time thing, the underwriter can count all of your income but if it's likely to occur again the underwriter has to reduce your income by the amount of the expenses from 2013.
It's really not a big deal and can easily be addressed through the LOE.
Take a look at the recommendations from some of my past clients on my Trulia profile by clicking the link below my phone number.
Please feel free to contact me for more information or help.
Senior Mortgage Banker
Lending in ALL 50 states
Great Plains National Bank