Actually, I think everything is ok. First, let's talk about Line 4a. Ignore it (I know, it is difficult to do so). In creating the simplified (?) Form 1040, the IRS collapsed two lines into one, and issued unclear instructions how to report pensions and IRA distributions. Turbotax has chosen an implementation, approved by the IRS, that does not include the pension amount in the Line 4a amount (it would include, say, an IRA withdrawal). Thus, it is $62,501 - $7,256 = $55,245, which is the amount reported by Turbotax. Also, $62,501 - $7,750 (QCD) = $54,751 which is the taxable amount shown by Turbotax.
To summarize, the total of all your distributions from qualified retirement plans is $62,501. All but the pension amount is shown on Line 4a. All but the QCD amount is shown on line 4b, which is the amount on which you are paying tax. So you are not paying tax on the QCD, as desired.
The social security benefit calculation is also correct. At your income level, 85% of your social security benefit is taxable. 85% of $43,596 is $37,057 as shown.
