Uncollected Employee SS/Medicare Taxes Box 12 W-2

Can someone tell us how you handle Uncollected SS/Medicare Tax. We have to go back and issue W-2's for termed employees that had Flexible Spending amounts that were ineligible so we have to show it as taxable income to the employee but we also have to indicate on the W-2 (Box 12 A & B) the uncollected tax amounts. Has anyone ever had to do this?