Filing married but separate. Have maxed out Roth IRA contributions but now says there's a 6% fee? How do I avoid this?

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If you lived with your spouse at any time during the year 2019, your max contribution is reduced or eliminated.

Ask the custodian to remove the excess contribution and its earnings.

[DianeC958]

If you are filing as Married Filing Separate and lived together during the year, the limit on the amount of income you can have on your return and take a deduction for contributing to a Roth IRA account is $10,000.
 

If you are Married Filing Joint and your income is less that $193,000 the you are allowed to contribute the full $6000 if your income  is between $193,000 to $203,000 then your contribution is limited and above the $203,000 you may not make a contribution to a Roth IRA directly.

If you are Single and your income is less than $122,000 you are allowed to contribute the full $6,000 if your income is between $122,000 to $137,000 your contribution is limited and above $137,000 you may not make a contribution to a Roth IRA directly.

Another option if you want to contribute the full $6,000 is for you to do a Back Door Roth IRA.

First you contribute to a Traditional IRA account and then you convert to a Roth IRA account, by doing the contributions this way you by pass the income limits and can contribute the full amount no matter how high your income is.

Amount of Roth IRA Contributions That You Can Make For 2019