When they make a correction, they put it on a W2-C. This stands for W2 Corrected. If they did not do that, but you can tell it is the new one, then you are fine.
Medicare tax will not affect your return.
Yes, if your wages were only $9,000 and you did not fill out a W4 for her to withhold more, then she actually did not need to withhold anything as $9,000 is below the filing threshold so there is no tax liability there.
She will not get in trouble.
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