On my 1099-R it shows the gross distribution and then the same for taxable even though I made a QCD. Why does it not deduct the QCD?

[SamS1]

Depends.  You need to be at over 70 1/2 to take the Qualified Charitable Distribution deduction for your withdrawal.  If you are at least 70 1/2,   TurboTax will ask whether a portion of your withdrawal was QCD under the Uncommon Situations screen directly after you entered the 1099R information in TurboTax Online.

[Critter-3]

The 1099-R was issued correctly ... the QCD is handled on the tax return ... follow the screens in the 1099-R entry section to indicate how much of the distribution was a QCD. 

[dmertz]

For those with a birthdate between July 1, 1949 and June 30, 1950, TurboTax presently (version R14.1) has a bug the prevents it from asking the necessary question regard transfer of the distribution to charity. As a workaround for this, with the CD/download version you can provide the QCD-amount information on the 1099-R in forms mode or in any version of TurboTax you can temporarily change your birthdate in TurboTax to something before July 1, 1949, edit the 1099-R form in TurboTax and answer the question asking how much was transferred to charity, then change your birthdate back in TurboTax back to your actual birthdate.