No, to paying taxes twice and to asking for a revised W-2.
When TurboTax detects an excess HSA contribution, then it immediately adds back the excess that come through the employer to your Other Income (look at line 8f on Schedule 1 (1040)). Alternatively, if the excess came from "personal" (i.e., direct) contributions, then the deduction number on line 13 (Schedule 1 (1040)) is adjusted to remove the excess.
If you received a 1099-SA with a distribution code of '2', then the amount in box 1 is ignored, because the taxation of that amount was already handled on your 2024 tax return (go see). Only the earnings (box 2) is added to Other Income on your 2025 tax return.
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