Because it was a single employer that withheld too much social security you will have to resolve the situation with them. The IRS will not issue a refund for over withholding of Social Security unless it occurs as a result of multiple jobs. It won't cause a problem with IRS and it shouldn't prevent you from filing your return. If you want to wait until it is resolved to file, you can file an extension. If you file an extension be sure to pay any federal and/or state tax you owe. The extension is only for the return, not the tax you might owe.
For information on filing an extension go to How do I file an IRS extension (Form 4868) in TurboTax Online?
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