Assuming that box 3 of the Form 1099-SA has code 1, did you indicate that the entire amount was used for medical expenses?
Are you itemizing medical expenses on Schedule A? If so, when TurboTax asks you to enter your medical expenses you must include the expenses paid with distributions from the HSA. TurboTax automatically subtracts from the total of the expenses entered the amount paid with distributions from the HSA.
