Adding the excess social security withholding was the right move. It is considered as withholding just like your federal withholding from your wages. If that has reduced your penalty to zero, because your total withholding reduces your overall tax balance due, then you can file your return without concern. Your actions accomplished what it should to include that excess as part of your withholding. Federal withholding (includes your excess FICA) is considered to be paid evenly throughout the year always.
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