If I understand you correctly, the code W amount for 2024 included the $642. The code W amount reports the amount that your employer sent to the HSA custodian for tax year 2024. It should not include amounts made in 2025 for 2024.
So you are saying that your employer made this contribution in 2024, yet when you were asked, "enter any contributions made in 2025 for 2024?", you answered $642, which had already been contributed.
It is unusual that an employer would make a contribution after the beginning of the year, yet include the contribution on the 2024 W-2. So the problem rests with your employer who added the $642 to code W and also told you that there was contribution for 2024 made in 2025, when their own paperwork says that it was made in 2024.
If your employer would have completed your W-2 correctly, this would not have been a problem.
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