This is a problem caused by the IRS' terminology.
The IRS considers the amount contributed by your employer PLUS the amount you contributed by payroll deduction to be the "employer contribution". So what you see is correct.
The reason for this odd treatment is that both the employer's contribution and your contribution by payroll deduction are combined into the code W amount in box 12 on your W-2, and are treated the same way, that is, the code W amount is removed from Wages in boxes 1, 3, and 5 on your W-2 before your W-2 is printed. This is why you don't see a deduction for your payroll contributions - your payroll contributions were never in your income in the first place.
Do NOT enter your payroll deductions on the screen headed "Let's enter [name]'s HSA contributions" on the second line where it refers to contributions "personally" made (see screenshot below). If you do that, you will overstate your HSA contributions on form 8889 and likely cause an excess contribution error message.
Yes, I know it is counter-intuitive, but this is the way the IRS wants it.
