It is supposedly a "helpful" notice (which is may not be helpful) , and does not change, or stop your filing of taxes in any way.
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It is likely just a calculation screw-up in the software (a BUG introduced in Wed night's update) ...that does not affect your taxes in any way.
Just edit each W-2 you entered, and make sure box 4 is entered to be the same number as on your paper/PDF W-2 from that employer. If box 4 is 6.2% of box 3...then nothing is wrong, and ignore that notice entirely.
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