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if you didn't file you can input these under Deductions & Credits / Estimates and Other Taxes Paid, it's not automatic, though some people have been complaining this topic doesn't come up in the interview flow.   if you already filed, what was the outcome - did you have less refund on your return, or have to pay more to the IRS then realize later it was wrong?  I think in this case you can just wait and see what IRS does to your return, they have a record of your ES payments and independently check for mistakes like this and recalculate underpayment penalties etc.

It sounds like you may be getting an error due to rounding on your 1099-Q.  My suggestion is that you round the amounts yourself before entering them.  When you do this, is Box 1 still the sum of Box 2 and 3?  If not, adjust Box 3 by $1 to make the math work.  This will not change your income tax liability.

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My conclusion….  The KY Form 740-PTET is not included in the forms included in the program.  You’d think if the program includes the calculations for the form it would be available to print but that’s not the case.  Talking with an individual who uses a professional tax package, her package didn’t support the form at all.  I just download the form from KY Revenue website and complete manually.  

is this Schwab by chance?  Certainly for Schwab, if an interest-bearing bond has OID, they report premium on 1099-OID Box 10 but that premium being reported is not fully related to OID, it's offsetting income on 1099-INT, so you can end up with Box 10 > Box 11.   I've also had issues with 1099-OID Box 10 at least on desktop it always flags an error and I would put 0 in Box 10 and enter it as an "Other" adjustment to the 1099-OID instead.  I think the adjustment can exceed the amount of the OID reported as long as you have other tax exempt income on your state return to offset.   If this is tax-exempt the outcome should not affect Fed taxes so I think you would input it in a way to get the right state tax adjustments.   Anyway, try putting Box 10 as $0 and enter the $391.42 as an "Other" adjustment and check your state tax outcome.   Not a CPA but that's been my experience dealing with this on Schwab 1099s.

I am the original poster. I edited the original post to reference the correct form.   Per IRS instructions, line 1 and line 3d should have the same amount. The TurboTax software is only pulling the 1099 amounts to line 3d, it is not reflected in line 1 and therefore the form does not generate the proper foreign tax credit amount.   Please tell me how this can be addressed by me or correct the software. An override prevents passing the Smart Check and prevents electronic filing.

@ sandra1990  The IRS website says that after the ID verification process it may take "up to 9 weeks" to process a return, but often it's sooner than that.   They say to wait 2-3 weeks, and then start monitoring occasionally at the IRS "Where's My Refund" tool. https://www.irs.gov/refunds