The way this works with HSAs is that when you take a normal distribution (code '1') from your HSA, TurboTax asks you if the distribution was used all, partly, or not at all for qualified medical expenses. If the distribution was used all for qualified medical expenses, then the distribution is tax-free. If the distribution was partly used for qualified medical expenses, then that part used for medical expenses is tax-free, and the rest is added to Other Income as well as taxed at an additional 20%. The same happens when none of the distribution is used for qualified medical expenses - it is all added to Other Income as well as taxed at an additional 20%.
So please go back to where you entered the 1099-SA and check how you answered the question about how the distribution was used. If you answered, "not used for qualified medical expenses", then the program is correct to add the distribution to Other Income.
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