One of the W2s received should be checked as "corrected"? If not, I would definitely suggest that you contact her employer and inquire as to why the 2 W2s as well as make sure they correct this error unless as I mentioned one W2 might have "corrected" checked at the top of it.
Clearly, there has been a mistake on their part and DaveF1006 is correct in that no NY return need be filed, only the MA return. Don't forget, as he states above, to have her put your address as the mailing address and her MA info as her residence.
