Your wife will need to file an amended return to correct the mistake. Wait until you receive her refund (and don't spend it all), before attempting to amend the return. It is somewhat likely that she will have to repay some of that refund when she fixes her return, because Married Filing Separately is generally a worse filing status than Single. Your other option is to file jointly, but that is even more complicated. If you choose to do that, I would consult a tax professional even before filing your return.
