Be careful about what your wife's status is for tax purposes, if she is a non resident or a resident for tax proposes. Usually, she becomes a "resident" after being in the country for 5tax years. If she was a non resident that year, she needs to file a 1040NR which limits the deductions she is entitled to: no standard deduction, no school credits! Furthermore, she cannot file a joint return with you unless there are some special provisions. I think you should contact the center for international programs at her school for advice on how to proceed when amending the returns!
Hope this helps!