The calculation of PTC with self-employed health insurance is convoluted and TurboTax cannot always calculate the optimal result for this situation. TurboTax uses the basic calculation provided in IRS Pub 974, but the IRS permits other ways that TurboTax does not implement for calculating the PTC and the self-employed health insurance deduction. This issue has been reported to TurboTax Product Qualify since 2015 and is unlikely to be changed in TurboTax, so if you have a different way to do a legitimate calculation of PTC and your self-employed retirement contribution, you might have to overrides and paper-file. You just need to make sure that the sum of your health insurance deductions (self-employed and Schedule A) plus PTC does not exceed your premiums paid and lines 14, 15 and 16 of Schedule 1 do not exceed net profit from self-employment.
[Edit] You might be able to get an appropriate result without using overrides by telling TurboTax that your self-employed health insurance was not through the Marketplace and specifying your self-employed health insurance deduction yourself, as long as you ensure that the sum of the PTC determined on Form 8962 and the self-employed health insurance deduction you entered do not exceed the amount of premiums paid.
