So you are saying that you received a 1099-SA but did not enter it in the TurboTax interview. Then it sounds like you understand what happened. Yes, the question "Did you use your Health Savings Account (HSA) to pay for anything in 2021?" might be better phrased as "Did you receive any 1099-SAs for funds distributed from your HSA in 2021?"
Once you go back into the HSA interview and say that you paid for something in 2021, you can enter your 1099-SA, and then the 8889 should be completed correctly.
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