You normally have a problem with the income not showing in wages if you didn't enter the proper dates for the acquisition and sale of the stock.
The stock must have been held at least one year and a day after your acquired it and at least two years after the original grant date for the gain on sale to be treated as capital gain income and for no ordinary income to be recognized. So, you need to make sure the dates you entered did not fall into that range for some of the income to be reported as wage income.
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