Was she in the US for all of 2018?
It sounds like they THOUGHT she was a Nonresident Alien that was exempt from Social Security and Medicare, but it sounds like she actually was probably a Resident Alien.
They can ask for her to repay the Social Security and Medicare taxes that SHOULD have been withheld, but I don't THINK they can legally require it (but not complying could cause problems at work). Or they can pay it themselves, and 'gross up' the amount paid (so you will pay income tax on the amount of Social Security and Medicare taxes they taxes for you).
It is the employer's responsibility to do payroll correctly, so THEY are the ones that need to correct it. If they don't know what to do, THEY need to consult a tax professional.
