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Whatever is reported on your W-2 is what is reported in the software.
But yes, if you had arranged for your employer to withhold extra federal taxes, those extra $$ would be included in box 2 of your W-2. Of course, it would be up to you to monitor your paychecks and paystubs to ensure the final numbers are correct.
Occasionally, people file a new W-4 with their employer to start extra tax withholding, but the W-4 doesn't get implemented by the payroll people, or is delayed a few paychecks before the increased withholding starts.
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