Retirement tax questions

IRS says that taxable SS was not calculated correctly,  they lowered the amount of the TT stated refund.  Also, since I discovered that my intended traditional IRA contribution was figured by TT as non-deductible and excess (no warning when 'Reviewed'!), and gave me a 6% penalty tax. I hadn't sent in the Traditional IRA yet, and won't, now that I see it isn't, according to TT deductible and excess.   I will have to file an amended to remove the forms 5329 and 8606 from the 1040 and get the 6% penalty returned, and not see an excess contribution going into 2025.

 

This really disturbing:

I received explanation from IRS about taxable SS being incorrect.   Indeed, using numbers off the TT filed 1040 and the IRS 1040 instructions Social Security Benefits worksheet,  I came up with taxable SS of 3236.    TT came up with 2214.  I don't know how that could happen.  It's pretty simple adding, dividing, and subtracting. 

 

What will make things worse is that TT deducted the non deductible, excess, undeposited, Traditional IRA from IRA distributions, so the number TT listed on line 4b is wrong. 

 

And, and,   I have no idea how TT came up with tax on line 16.  Income of $6134 on line 15 should be, from tax table, $613,  not the $184 shown by TT.  How did it do that?  And how is it IRS didn't find this?

 

Am I missing something(s?) here?

At this point, after correcting the SS amount, taxable IRA distributions, and correcting Tax amount, I may owe money rather than the TT promised refund.