No, they should not be.
Your employer deducts the amount that they pay you as salary on their tax return. They also get to deduct any employee benefits that they pay, which in this case is those matching contributions. If they are deducting them twice then they are making an error. You will also be paying taxes on the contributions both when they give them to you as well as when they are paid out of the account, as you said.
You need to contact your employer and request a corrected W2.
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