I filed a paper return in 2019 that was processed only now. In my return, I opted for a standard deduction which naturally lowered my taxable income. I paid the taxes in full. When I checked my transcript online, IRS seems to have ignored the standard deduction making my taxable income the same as my AGI thus increasing my tax bill. Furthermore, they charged me a penalty for the amount owed.
I'm not sure what exactly happened, but this seems like an error at their end? How can I rectify this?
