If I understand correctly, you filed your return and have your refund back but the W2 you used had the incorrect social security number. So basically your tax return is correct the W2 however is incorrect.
Contact your employer and have them issue a corrected W2. Eventually the IRS would catch the error, but if they can issue the corrected W2 quickly it may all sort out. You should not amend your return as it is correct. .
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