Retirement tax questions

To follow up on this issue, my federal returns look fine for backdoor IRA, however in my MA state return, schedule X shows this amount as taxable roth IRA distributions and when i look back state return line 9 that amount me and my wife contributed $12000 is added to line 3 which is wages and tips, salaries. So am i being taxed twice here for MA state returns? 

I can't even remember how i did the taxable ira/keogh section now. I was under the impression it was automatically transferred from the federal returns and filed it. 

What should i do or enter to make sure this $12000 is not being added as taxable income on the online software and how can I amend it? Please help!!