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Retirement tax questions

I made $2250 excess ROTH IRA contribution in 2017 and withdrew the excess contribution and earnings, $158 early April, before the due day. In Feb. 2019, I got the 1099-R. Since the earnings are taxable in 2017, I'm amending my 2017 tax return for this taxable income. Unfortunately, there is a new excess in 2017 due to the income change. I was wondering if I have to pay 6% penalty for the new excess which I just discovered for 2017.  Do I have to pay 6% penalty for the new access for 2018? If yes, what I should do in TT when I file my 2018 tax return. Thanks!