"For the 2023 return, TurboTax included the earnings amount $50, which corresponds to the number in box 2 of the 1099-SA, on line 8f of Schedule 1 (1040). Could this result in an overpayment of taxes?" No, this is not an overpayment of taxes. It should be reported here.
"Additionally, should I still withdraw the amount listed in box 2 of the 1099-SA from my HSA to avoid receiving another 1099-SA from this account next year?" I don't think you will receive another 1099-SA next year from this, but you will have to ask your HSA custodian (who I suspect will be quite confused as to the question).
If you don't expect to receive another 1099-SA on this earnings amount, I would let it go. This is getting into de minimis territory, which is tax legalese for "not big enough to make a big deal out of".
Like I said, just document everything you did and why, print it, and stick it in your tax file, in the unlikely event that someone asks about it. Even in the unlikely event (as I said) that someone does, the amount of money to fix the problem in a few years will still be, well, de minimis...
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