They are not taking the second stimulus payments out of your tax return. When you prepared your tax returns, you were asked how much you received for the first and second stimulus payments. Your input in these fields was used to determine if you were eligible for the Recovery Rebate Credit.
If you met the criteria for the credit, you received it when you prepared your 2020 income tax return. The credit is intended to give those who should have received a stimulus payment but never did a tax credit on their tax returns. Any excess credit is then refunded to you if there is an overpayment on your tax return.
Please see the attached link for more information on who can claim the credit.
Recovery Rebate Credit eligibility
If you indicated you did not receive either of the stimulus payments but you actually did, the IRS is pulling these returns aside to reconcile the credit. They will issue notices directly to you if they determine the returns were not completed correctly. You do not need to amend your return.
Correcting Recovery Rebate Credits on returns already filed
@sherlynn02
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