The Form 1099-R is correct. The fact that some or all of the distribution represents a QCD is reflected on how the income is reported on your tax return. Nothing about the information on a Form 1099-R is permitted to show that a QCD is involved but is instead required to report the distribution the same as any distribution paid to you.
When you enter the From 1099-R that reports a distribution from a traditional IRA and you were age 70½ or older at some point during the tax year, TurboTax will ask if any of the distribution was paid directly to a charity. If you answer Yes, TurboTax will ask how much was transferred to charity. TurboTax will then include the entire amount on Form 1040 line 4a but will exclude the QCD amount from the taxable amount on line 4b and will include the "QCD" notation next to this line.
Make sure that your marking of the IRA/SEP/SIMPLE box on TurboTax's 1099-R form reflects the marking of this box on the Form 1099-R provided by the payer.