Excess contributions result from contributions. Forms 1099-SA report distributions, not contributions, so entering a Form 1099-SA cannot cause TurboTax to generate a penalty for an excess HSA contribution. However, the same HSA section also asks about HSA contributions, so you have probably moved beyond the entry of the From 1099-SA before causing TurboTax to indicate an excess contribution.
Until you properly complete the HSA section of TurboTax to establish your eligibility to make the HSA contribution, TurboTax will treat any HSA contribution entered, either with code W in box 12 of TurboTax's W-2 form or as a personal HSA contribution, as an excess contribution. You can also have an excess contribution that carried in from the previous year. Eligibility for an HSA contribution is established by indicating what months you were covered by an HDHP and no other, disqualifying coverage such as Medicare, and that you cannot be claimed as a dependent on someone else's tax return.
