FICA limits when your income is from two jobs?

 If you're overpaying, the Internal Revenue Service offers a solution. You may claim a refund of the overpayment Line  of Form 1040, the individual tax return. The IRS will issue a full reimbursement of the overpayment, as long as you don't owe any income tax. If you do owe current-year or previous-year taxes, the IRS applies your overpayment to that amount first, then issues any balance to you.

Your employer may claim an overpayment from the IRS as long as he reimburses the employee as well for the excess payroll tax. The employer must file an adjusted business tax return, and the IRS will then apply the overpayment as a credit on any future taxes due.

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"you may be able to claim the excess as a credit against your income tax on your income tax return. Use either Worksheet 3-1 or 3-2 in Publication 505, Tax Withholding and Estimated Tax (PDF) to help you figure the excess amount."

When you file your income taxes you can get excess social security to reduce an income tax liability due, or increase a refund due.

This is how you get any extra social security taxes. When you enter your W-2s any tax software should be able to deal with this excess social security taxes withheld and properly credit you for this.