You can only deduct expenses that were paid out of pocket. You can't deduct expenses paid with insurance or from a tax-free account such as an HSA, MSA or HRA.
However, I suspect that Turbotax is written to assume we are all dummies, and I think that if you review the health care deduction interview, you will be asked first to list all your expenses, regardless of who paid, and then as you continue you will be asked to enter the amounts of tax-free reimbursement and HSA account withdrawals used to pay expenses. Then Turbotax will do the subtraction for you and only claim a deduction for expenses that were non reimbursed tax-free.
