@besito89 , are you on F-1 and is that why your spouse is on a dependent F-2 visa? Which country are you each from ? When did you first enter this country with F-1 ( five years ago or what ? )? What is your visa status now? As a student why do you need to file jointly ?
Some of these questions ( which I would like answered) may or may not affect my answer but these do give me the full back ground, so, please answer as many as you can--yes?
As far as the rejection by the IRS of the application ( not properly filed ), I would suggest visiting the local IRS office ( or the nearest ) and ask them for help including certifying a copy of the original passport to satisfy the documentation requirements.
If you filed jointly and asked for ITIN issuance retroactively, you would have to amend your return to Married filing Separately IF you are still Non Resident Alien because 1040-NR assumes single / married Filing Sep. However , if you have passed the SPT and therefore a Resident for Tax Purposes, then yes , you do file on 1040 , can use TurboTax and indeed can file joint with your spouse if and only if the spouse has a tax ID ( SSN / ITIN ).
Once I hear from you on my questions, I will circle back
pk
