Retirement tax questions

As for line 4a:

Taxpayers assume that 4a should be the total amount of IRA/pension/annuity distributions and 4b should be the taxable amount, but that is clearly not what the IRS instructions call for.

You can see for yourself on pages 28 and 29 at https://www.irs.gov/pub/irs-pdf/i1040gi.pdf for lines 4a and 4b.

"Except as provided next,
leave line 4a blank and enter the total
distribution (from Form 1099-R, box 1)
on line 4b."

There are multiple exceptions listed ("except as provided next") in the text that follows, in which you are supposed to add the total distribution into 4a, not leave it blank as stated above. This means that sometimes the total distribution of an IRA/pension/annuity is added to 4a and sometimes it's not.

This was tolerable while IRAs were reported on one line and pensions/annuties on another (yes, this is the way it has worked for years), but in 2018 when the IRS redesigned the 1040 form, they lumped IRAs and pensions/annuities together on one line.

Now we see much more often that some of the total distributions are added to line 4a and some are not, with the result that 4a is sometimes smaller than 4b.

This surprises a lot of taxpayers, but it is exactly what the IRS instructions call for.

As for line 4b:

The amount in box 2 on a 1099-R is usually the taxable amount of a pension distribution, but not always. In the 1099-R, if you are asked if this plan is a qualified plan, then you are led through a series of questions which ask for your basis (after-tax investment) in the plan. Depending on how you answer these questions, TurboTax may use the amount of taxable income that it calculated instead of what's in Box 2a (usually using the Simplified Method - see https://www.irs.gov/taxtopics/tc411). 

That is, the pension administrator may not be aware that you have basis in the plan and will put the entire amount of the distribution as taxable in box 2a, whereas your answers may indicate to TurboTax that your taxable amount should be less. This is especially true when pension plans are sold to new administrators; each taxpayer's basis in the plan does not seem to be passed on (you are responsible for keeping this information).