It is an entry issue. Since you have a QCD from your IRA the amount that went to the charity is not taxable and would not show on line 4b.
The amounts in Box 1 and Box 2 of your 1099-R should be different based on the amount of the QCD. The amount in Box 2 carries then to Line 4b and adds to your taxable income.
If you have basis in the IRA there should an amount in Box 9b the amount is your basis in the IRA, if that amount is there TurboTax will calculate the taxable amount using that information.
Link to more information about IRA Frequently Asked Questions
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