Yes, there will be a form 8889 on her return, because of the code W in box 12 of the W-2. NOTE: the code W amount is the sum of what her employer contributed plus any amount she contributed by means of payroll deduction.
Yes, this is called the "employer contribution", but that is a reference to how the contributions are handled, not to whom made the contributions.
Since the 8889 will be added to her return, in her Review, there will be the Self/Family question. As I said, just choose Self as a workaround for this question in the Review.
When she contacts the HSA custodian, be sure that she asks for "withdrawal of excess contributions" so that the custodian's paperwork will be correct.
NOTE: there may be a form on the custodian's website for this.
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