All funds contributed by payroll deduction, whether employer assistance or voluntary salary reduction, are considered "employer contributions" for tax law.
If you have an excess contribution, and you need to remove the excess contribution, there is no difference between money contributed by the employer, the employee, or money contributed by you directly out of pocket. You just specific a dollar amount, and the HSA bank returns that to you, along with any earnings. The amount is added to your taxable income because it is not deductible.
