"But the instructions are wrong."
Whose instructions are you referring to? The IRS' instructions for the 8889?
Pay periods that span the end of the year do present an "opportunity" where the employer puts the final HSA contribution in the books for one year (say 2020), but the actual HSA contribution is done a few days later in the following year (2021).
And you have to hope that the person doing the paperwork notes that the next year contribution was actually for the previous year. The benefits company used by my spouse's employer has not always been so careful.
The IRS instructions do presume that the code W amount does not contain any 2021 contributions for 2020.
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