Did you e-file or mail your tax return? If mailed, the IRS data transcriber (a person) could have failed to transcribe the QCD notation. (It's not real apparent on the printed form unless you are looking for it.) Otherwise, perhaps the tax return was for some reason examined by an inexperienced examiner who failed to recognize that the gross amount was present on Form 1040 line 4a but excluded from line 4b with the QCD notation. You might download the transcript of your tax return to see if it mentions the QCD notation.
https://www.irs.gov/individuals/get-transcript
Given that the IRS has questioned the reporting, your response needs to indicate that the gross amount of the distribution was included on line 4a and that the QCD notation was included next to line 4b to indicate why the taxable amount was less than the gross amount. It would be prudent to include your supporting documentation showing that the IRA paid the funds directly to the charity and that the charity acknowledged receiving the funds.
