My wife's W-2 was mistakenly applied to me, which led to $1,764 of excess Social Security tax being improperly deducted on our 1040. The IRS sent me a notice asking for the full $1,764. However, we received a refund of $1,141 that year. If we had not taken the deduction, we only would have owed $623 in tax. Why isn't this the amount we have to pay the IRS?