Whenever tax is estimated and withheld, it may not actually match the tax that shows on your tax return.
If you are talking about gain from the sale of employee stock, the amount of tax withheld would be on your W-2 form, so I would expect a change when the stock transactions are entered.
If that is the case, you would have entered the tax withheld first and then the taxable event later when you entered the 1099-B.
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