Because we get into answering this, we need to know some things.
1. You are referring to a 1099-SA, not a 1098-SA or anything like it (like an SSA-1099 or any 1098)?
2. Box 5 on the 1099-SA is not the distribution code - this is in box 3.
3. 1099-SAs with regular distributions and/or earnings in excess contributions, are not tightly tied to a tax year in TurboTax. That is, the distribution code of '2' just reports an amount to be added to taxable income for the current year, no matter if the 1099-SA was generated by events in the current year or the previous year.
4. Did you not receive two 1099-SAs: one with a distribution code of '1' and another with a distribution code of '2'? I think that the confusion is rooted in the fact that you got one and entered it, and not the other.
Please confirm the amounts in all the boxes in your 1099-SA.
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