The amount contributed to charity as a QCD must also meet the charitable contribution requirements that would be necessary for it to be deductible on Schedule A were it not made as a QCD. Documentation that would support this as a QCD would be anything from the charity acknowledging receipt of the contribution and any documentation from your IRA custodian that would show that the distribution was made after you actually reached age 70½ and was paid directly to the charities.
If you paper-filed your tax return or a person at the IRS examined your tax return for some other reason, they could have simply missed the "QCD" notation which is all that is necessary to appear on your tax return.
On Form 1099-R the payer reports QCDs the same as any normal distribution, code 7. There is no special coding for a QCD because the payer cannot know for certain that the contribution qualifies as a QCD; only you can know that.
