I had my salary through 1042-S (tax treaty) that I entered as suggested in the miscellaneous incomes. Now I am paying 6% penalty for my ROTH IRA as no income is detected?

Turbotax says my income is $0 since does not detect it from the miscellaneous incomes that I had to add both in positive and negative values since I was paid under tax treaty. I contributed to my roth IRA last year but now I have to pay a penalty because it's higher than my wage. How can I avoid this issue?