When you prepare the amended return, you can enter a negative adjustment to income to remove the additional income reported in error.
Also, the income reported on your W-2 is taxed as ordinary income versus capital gain income reported on the stock sale. If you factored the income reported on the W-2 into the cost basis of the stock sold, by adding it to the cost, your overall loss would be the same as if it had been reported properly. It may be that you pay more tax since some of the loss is being reflected as ordinary income that is then offset by a capital loss. But the overall loss reported would be the same. So, I'm not sure if there will be that much of a difference when you amend the return.
You can make that adjusting entry in TurboTax as follows:
1. From the Federal menu in TurboTax find Wages and Income
2. Find Less Common Income
3. Choose Miscellaneous Income, 1099-A, 1099-C
4. Choose Other Reportable Income
5. Enter a description of the adjustment and the adjustment as a negative number
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