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I realized my mistake! There are two boxes: one for the total of employer + employee contributions, and one for "employee contributions (not through employer)". I misunderstood this second box to be asking how much I personally contributed out of the total. I think this instead for cases where you contribute outside of paycheck contribution. I updated this box to "$0" and it solved the problem.
No, you should not be charged a 6% tax based on the information you provided.
Did you include amounts withheld from your paycheck as "Any contributions you personally made"? Amounts you "personally made" don't include withholding from your paycheck. This should only include amounts you sent directly to your HSA. If you entered your W-2, your contributions withheld from your pay are already included in your tax return, so entering them again is double-counting them.
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