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Not sure what you mean. The amounts in boxes 4 and 6 are never refunded to you, nor do they factor into the calculations of your tax due or refund unless in an uncommon situation a person had excess Social Security withheld.
I suspect that what you are really seeing is that adding your spouse's W-2 did not increase your refund and might even be causing you to owe.
WHY DID MY REFUND GO DOWN WHEN I ADDED ANOTHER W-2?
You started off with your first W-2 and your refund looked high? Then you added another W-2 and it stopped looking so good? That is normal. When you added more income, your tax liability increased, so you saw your refund decrease. The program began by giving you your standard deduction—- which lowered your taxable income. (if you are filing joint it took $25,900 off your income right off the bat) So you are not being taxed on as much of the income on that first W-2. Then you added taxable income--so the refund went down. Your refund (or tax due) is based on the total of your income, not “per W-2.”
And…adding income may affect other credits you were getting like the earned income credit.
Wait until you have entered ALL of your income and credit/deduction information. You can't really tell anything until it is all entered. That “refund monitor” does not mean anything until everything has been entered.
https://ttlc.intuit.com/questions/2273878-why-did-my-refund-drop-when-i-entered-another-w-2
No, there is not a bug. The amount that is deducted from your paycheck for Social Security tax in Box 4 and Medicare tax in Box 5 does not go towards your tax liability. The only time it would affect your taxes is If either you or your spouse had more than one employer and excess Social Security or Medicare was withheld, or your employer withheld too much. If this is the case, TurboTax automatically adds the excess that was withheld to your federal tax refund or will subtract if from your balance due.
For more information, please review the TurboTax article Video: What Is Social Security Tax?
[Edited 02/26/23|10:34 am PST]
The amount in Box 4, Social Security tax withheld and the amount in Box 6, Medicare tax withheld are never, ever counted as withholding, (Box 2). They are used to pay your Social Security and Medicare at retirement.
There are sevreral factors that can cause Box es 3 and 5 to be different from your Box 1 wages. A ciommon one is having contributed to a retirment plan. In this case you are taxed on your Box 1 wages, which would be less than Boxes 3 and 5.
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