It is likely they did pay the taxes, as they need to report the wages for each quarter on a Form 941 and pay in the FICA taxes due on those wages, both employer and employee portion. If they didn't pay your share, the IRS would inform them that the form was not correct and bill them for the missing taxes. It is their job to collect the taxes from the employees, and the amount due is their responsibility. They can't just not pay your share, as they owe that amount whether they collect it from you or not.
I don't know of the legality of taking taxes out from current wages to make up for not taking them out from previous wages from which they were owed. You had an obligation to pay your share of the taxes, but they had an obligation to collect them. That would be a civil matter between you and the company.
As far as the W-2 is concerned, if the missing FICA taxes are not listed in boxes 4 and 6 on your W-2 form, it should not impact your income tax in any way. So you may be able to file the tax return with the W-2 form you have without it affecting your tax.
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