Did you receive a form 1099-SA? This is how qualified medical expenses are reported to you, and you enter this in TurboTax in the HSA interview.
What do you mean "you filled out a 8889 and got a totally different figure?" Because of the counter-intuitive terminology that the IRS uses for HSAs, it is highly unlikely that a non-tax professional is able to fill it out correctly by hand.
So tell us what lines were totally different on TurboTax's 8889 and your 8889 - line numbers and dollar amounts.
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