There's a 5 year exempt period for a student on an F1 visa (and student's spouse F2) and therefore ineligible to file the 1040 and ineligible to file jointly.  Check Pub 519 if there are any exceptions to allow them to presume otherwise, don't recall without looking it up.

***Should add, except for students from India and I remember one other country...used to prepare many 1040NRs but it's been years now.  Check the tax treaty publication too.