This is an employer issue. If they improperly withheld FICA taxes, your spouse will need to contact her employer to fix this. There's nowhere on the tax return to claim a refund on this type of mistaken withholding.
Whether or not your spouse's income is subject to FICA depends on her visa status, not whether or not she can elect to be treated as a resident for tax purposes. Please see the information on this IRS website.
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