Yes, it is forcing certain taxpayers to enter the HSA reimbursed amounts in Schedule A.
"I had a 1099-SA for medical expenses I was reimbursed for and did not enter those medical expenses in TurboTax. "
Yes, TurboTax assumes that you will list all medical expenses in Schedule A, and then add insurance reimbursements. The problem is that TurboTax automatically adds the amount of expenses as shown by the sum of 1099-SA expenses to subtract them from Schedule A, i.e., just like the insurance reimbursements. So few people itemize medical expenses any more than this doesn't seem to be much of a problem, but for the few who do use the HSA AND try to deduct medical expenses on Schedule A, as you see, this can cause issues.
A way for you to address this is to not add the individual HSA medical expenses in Schedule A, but to add up all the HSA distributions for medical expenses, and add a single medical expense for Schedule A as a Miscellaneous expense, so that it offsets the automatic entry for HSA reimbursements.
Does that make sense? The IRS won't care, and will be happy that the Schedule A numbers are correct.
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