The IRS unfortunately did decide at some point to include the employee’s pre-tax deductions as “Employer Contributions” (leading to many a discussion like this).
@Paresa, here it is from the horse’s mouth, in the instructions for Form 8889. As DawnC said, you probably just need to make sure your high deductible health plan coverage is entered (unless there’s a double-entry of the cafeteria plan amount, and it’s also appearing as a contribution you personally made, on the “Let’s enter your HSA contributions” screen...).
If you’re still getting an unexpected result though, be sure to re-post, and we’ll figure out what’s going on!
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