How to correct the error that even though the entries are correct, but Tubotax deluxe takes the taxable income from Box 1 and not from Box 2a?

Delete the 1099-R and then re-enter it.   After you enter it, you will need to answer the follow-up questions to calculate your tax, if any, on your tax return.    Where do I enter a 1099-R?   Go all the way through the retirement income section.  

How to delete forms in TurboTax Online

How to delete forms in TurboTax Desktop

I tired deleting the 1099-R and adding it again.  However, it still does not take the entry from Box 2a but takes it from Box 1 even though Box 5 shows the employee contribution.  I tried event o force the correct amount by adding it manually, but it did not work.

I tried deleting the 1099-R and adding it again.  However, it still does not take the entry from Box 2a but takes it from Box 1, even though Box 5 shows the employee contribution.  I tried even to force the correct amount by adding it manually, but it did not work.

Within the pension distribution entry screens, you want to reach the screen We found a few other questions about your situation.

The questions that follow may allow you to use the simplified method to determine the taxable amount for box 2a.