"what should I do in turbotax to avoid paying the extra 6% penalty on the excess contribution for 2023?"
When you were told by TurboTax that you had an excess, TurboTax asked you what you were going to do. If you said, "Withdraw the excess before the due date" (which I think you did), then there will be no carryover and no 6% penalty.
Enter the 1099-SA with the distribution code of 2 in your 2024 tax return. Your entries on your 2023 return will cause the excess through the employer to be taxed, and the 1099-SA on the 2024 return will cause the earnings to be taxed in 2024 (which is correct).
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