Agree on (a) the second employer should have withheld (it's noted on the SS website, and the IRS and SSA have a reconciliation/reporting requirement in Section 232 of the Social Security Act, and you may have inadvertently created a problem for them by not withholding), and (b) I would simply put $0 on your second W-2 for SS withholding -- it may trigger scrutiny but if the numbers line up, probably nothing more for you. (Normal practice going forward and the "right' way to do this is simply to have double SS withholding and then claim a refund for the excess amounts -- very common.
Want to make sure, though, that your second employer did withhold Medicare. There is no double-withholding out, and you might have a real tax liability along with your employer if it did not.
