When you run the HSA interview on the Deductions and Credits page, there is a screen that asks "Did your employer tell you about any additional contributions (this is uncommon)." And you can enter 2024 contributions that were designated for 2023 or 2025. That should clear the issue for this year. (If the withholding occurred in 2024, your W-2 is correct, so you make the adjustment in Turbotax on the page I described.)
I'm not sure what will happen in 2025, you will have to wait and see how the rejected contributions are handled on your 2025 W-2.
