Your Federal Taxes should not change significantly IF the taxes withheld on the stock sales match the taxes due. Your broker may have estimated the taxes based on an average while you owe taxes at different rate.
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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