You may have made an entry to adjust your reported cost basis and that is affecting your gain or loss.
You can adjust your cost basis because it was reported wrong on your form 1099-B. If so, you will see a screen after you enter your investment sale information that says Select any less common adjustments that apply, on which page you will select The cost basis on my statement in incorrect and then be instructed to enter the correct cost basis.
The entry you make there will become your new cost basis and the difference between that amount and your original cost basis will be entered on your form Schedule D Capital Gains and Losses. Your gain or loss will then be the difference between your proceeds and the new cost basis that you entered.
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