First the program could be correct ... the IRS could be wrong.
In the interview in the 1099-R section you had the option to either enter the amount in box 2a yourself or let the program calculate the taxable amount by answering some questions which is probably what you did. Usually the amount that is listed in box 1 would be the same as box 2A UNLESS box 2b is checked. You would need to review the form 1099-R and what you entered in the program against what was listed on the 1040.
Turbo Tax is a self prepared return. It has no way of knowing or checking that you entered something wrong or in the wrong place or entered something twice Or left something out. It doesn't check against any outside sources. The IRS has copies of all the W2s and 1099s your employer and banks/brokers, etc. sent in to match against. Turbo Tax only checks the calculations of what you entered. It is your responsibility to check it over before you file. They only Guarantee that the calculations are right based on the entries you made.
Any calculation errors on the part of TurboTax are covered under the Accurate Calculation Guarantee. TurboTax will pay any penalties and/or interest due to a calculation error but not any taxes owed. The Guarantee does not cover any user entry errors or omissions.
See this TurboTax support FAQ for the 100% Accurate Calculation Guarantee - https://ttlc.intuit.com/questions/2566201-what-is-the-turbotax-100-accurate-calculation-guarantee
See this TurboTax support FAQ for submitting a claim - https://ttlc.intuit.com/questions/1901269-how-do-i-submit-a-claim-under-the-turbotax-100-accurate-ca...
