As Opus 17 indicated, due to the way TurboTax handles HSA distributions, if you are itemizing medical expenses that were not paid with a distribution from the HSA or FSA, you must include in the medical deduction section those expenses paid from the HSA in addition to entering the Form 1099-SA in the HSA section. TurboTax automatically subtracts the amount reported on the code-1 Form 1099-SA from the total medical expenses entered before including the rest of the medical expenses on Schedule 1.
Nothing about expenses paid from the FSA goes anywhere on your tax return.
