You are filing an federal income tax return, not a FICA return.
TurboTax takes the amount that your employer put on the W-2. TurboTax doesn't calculate the FICA tax (Social Security and Medicare taxes on the W-2), except to check if the SS tax is too high (if so, TurboTax warns you to check that). If it is, TurboTax - depending on the circumstances - may be able to adjust this on the tax return (but can't always).
I see no reason why your income tax return would be wrong, if only the FICA were understated. The company needs to work out their response with the IRS. This may involve a letter from the IRS asking you to pay the understated amount (but let the company work on it first).
