It sounds like the withholding was included in your spouses' W2 from ISOs or RSUs at the time of sale. This happens when some of the vested shares are sold to pay the taxes for the vested shares. You are not being taxed twice.
You should look at the documentation at the time the shares were awarded to see if these withholdings are already included in the W2 which is most likely. The amount of taxable income will become the stock cost basis in the shares held until they are sold.
Once you have the rights to the shares, through the vesting period or through the purchase of ISOs o the exercise date, then there can be taxable income included in the wages for the employee stock.
Please update here with questions if you need further assistance.
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