When entering medical expenses should I include things that I paid for with my HSA? I entered ones I didnt pay with my HSA but now it wants me to confirm my HSA was used.

Note that the way that TurboTax is designed, you are intended to enter all medical bills whether reimbursed by insurance or an HSA/MSA or not into the Medical Expenses dialogue. Then, when you enter the insurance reimbursement at the end of the dialogue and when TurboTax automatically brings over the HSA distribution for medical expenses, then the result should be only those medical expenses that you paid with after-tax dollars.

As a result, taxpayers who have HSA distributions but who also had so many after-tax payments that they would also qualify to deduct something on Schedule A, need to enter a dummy entry in the other medical expenses at the end of the Medical expenses interview. The entry can be as simply as "HSA expenses" and the amount of the distribution that went to qualified medical expenses (probably the entire distribution).

In this way, when the HSA distribution is brought over automatically, it won't artificially reduce your Medical expense deduction.