I recommend reviewing your input again. Start with the federal interview section of the program under the Business tab and review the entries in each screen.
Once you have done that, proceed to the State Taxes tab and go over the state interview questions again. It's possible the a box may have been accidentally checked or an answer was answered incorrectly.
If you did have self-employment income, MA does allow you to deduct up to $2,000 in self-employment tax on your state return.