No, once you extended your return, you had until October 15 to withdraw the excess, although you might have to fight the HSA custodian a bit about the withdrawal being after April 15th.
"I already filed to IRS of that extra $1250 as my other income for tax year 2022" - Are you saying that you manually adjusted your 2022 return to add back that $1,250? The moment that the excess was discovered by TurboTax, TurboTax added the excess back to Other Income, assuming that the excess was from the code W amount in box 12 of your W-2.
"what to do with the form 1099-SA I received afterwards, should I just skip or fill in all the information into Turbotax to pay tax possibly twice?" - Does this 1099-SA have a code of 2 in box 3? If so, only the earnings in box 2 are added to your income; the amount of excess in box 1 is ignored, because TurboTax knows that the excess was already handled.
Does this cover your situation?
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