I am a non resident alien, married a US citizen in Aug 2013, currently applying for Green Card. My wife (US citizen) is filing her tax through her CPA, and found that she will have to pay $48 to the IRS. My wife is a full time student and works a full time job at a bank. She was taxed heavily on her bonuses and her paychecks as usual. So of course we were shocked! On contacting the CPA, he is saying that she can file as single, in which case she will get back $3000 as tax refunds. Now all these just doesn't make sense to any of us. Is the CPA making a mistake? Should we get a TurboTax package and file it on our own?
As a side note, if it is of any use, I am a full time grad student, and my school provides tax filing software for free. I filed my tax as married (as the software asked me whether I was married as of the last day of 2013) and I am getting the usual ~$500 back.

