Excellent!
Yes, it is certainly an issue when the employer makes the HSA contribution after the first of the year, and may or may not tell the HSA custodian that it is for the previous year (the default is to assign the year in which the contribution was made).
The Box 3 instructions on the 5498-A says, "Enter the total HSA or Archer MSA contributions made in 2024 for 2023." This is a perfect example of a contribution made after the first of the year for the previous year.
As you can see, the 5498-SA doesn't exactly line up with your tax returns. For example, box 2 says (among other things), "Enter the total HSA or Archer MSA contributions made in 2023. Include any contribution made in 2023 for 2022." The contributions made in 2023 for 2022 don't appear on your 2023 return - a great source of confusion.
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