I too am having this problem. I have only entered the above and beyond medical expenses paid in addition to what HSA account paid. But at the end of process TurboTax deducts the amount listed in the 1099-SA and states if amount is incorrect to go back to Wages & Income and edit your form 1099-SA. This does not seem correct as the amount that I paid out of pocket was significantly greater than what was paid from HSA by over $7K because I didn't have the funds in the HSA account.
