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Other tax discussions

While filing my 2017 married jointly tax return, I received this reject code IND-032 from the IRS saying that my spouse's 2016 adjusted gross income (AGI) was incorrect in their records. So I did some digging and figured to request my spouse's IRS tax transcript and it turns out the AGI on the transcript is the same AGI we initially inputed before the rejection. 


Here's a bit of background from 2016. My spouse and I married late 2016. Since I was still a dependent under my parents for most of 2016, I filed married separately. My spouse on the other hand, accidentally filed married jointly. We then quickly amended my spouse's tax return to married separately. 


Any help would be much appreciated as I will be calling the IRS to ask also but I thought I would post an enquiry here!