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Your employer should refund the money they took from your wages. They probably also withheld Medicare and Social Security tax that also needs to be refunded to you.
If your employer refuses to refund the monies they took from you:
Note: Keep records of phone calls, emails, everything related to getting this situation corrected with the employer including the payback issue.
Use IRS Form 843: Claim for Refund and Request for Abatement and Form 843 Instructions to prepare.
Social Security and Medicare Tax states:
If Social Security or Medicare taxes were withheld in error from pay that is not subject to these taxes, contact the employer who withheld the taxes for a refund.
If you are unable to get a full refund of the amount from your employer, file a claim for refund with the Internal Revenue Service on Form 843, Claim for Refund and Request for Abatement. Attach the following items to Form 843:
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