For line 3a, the IRS instructions say, "Line 3a. Enter the following itemized deductions (from Schedule A (Form 1040)) on line 3a. • Medical expenses (line 4). • General sales taxes (line 5a). • Real estate taxes for your home (line 5b). If you don't itemize deductions, enter your standard deduction on line 3a."
It used your HSA distributions, not your HSA deduction, because TurboTax assumes that the distributions reported in box 1 of the 1099-SA correspond to medical expenses that you paid for.
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