What you see on your paycheck stub is your employer withholding the money for the 0.9% Additional Medicare Tax, as it was required to do by law.
What you're seeing on your return is the assessment of that tax.
That's how it works -- it's similar to the normal withholding on your Form W-2 to help offset the tax on that income reported on your return.
Here, instead, this 0.9% withholding is designed to offset the 0.9% tax assessment on your return for Additional Medicare Tax, so as not to actually increase any tax burden come tax time.
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