Box 7 is your social security tips. Box 7 and box 3 should equal box 1 for your total wages. Social security should be withheld on box 7 as well as box 3. So she is actually right.
Basically as a tipped employee, your wages are accounted for slightly different on your W-2, as they are split up, but it is all still subject to SS. If you multiply box 1 (assuming you have no retirement or other benefits that is not taxed) by 6.2% you should still come up with the right amount.
When you enter everything in TurboTax does it tell you that you had too much withheld?
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