we can't see the IRS notices, the original return, W-2c, or the amended return you filed.
as a guess when you filed the amended return did you reflect the refund from the original return.
did you send in the amended return before the original return was fully processed? this can cause issues. especially since the corrected w-2 from the employer goes first to the Social Security Adm (same as the original) and then it must send updated info to the IRS
someone would need to review all the filings and documents to give you an explanation. the IRS could be wrong. hiring a pro would likely cost more than the $90 so call the IRS to get a clear explanation (if they can provide one). Turbotax gets no additional info once a return is accepted so they can't help.
