This is correct.
The IRS
considers both your employer's contribution to your HSA PLUS your contribution
to the HSA by means of payroll deduction to be the "employer contribution".
The amount on line 9 on form 8889 should be equal to the amount on your W-2 in box 12 with a
code of W.
The
amount on line 2 should be equal ONLY to the amount you sent directly to the
HSA (not through your employer); note that most taxpayers do not do this.
The
amount in box 12 with a code of W is removed from Wages in boxes 1, 3, and 5 on
your W-2 before it is printed. This is why you don't see a deduction on your
return for your HSA payroll contributions - because they were never in your
income in the first place.
So the HSA Summary is just using the IRS's own terminology, no matter how counter-intuitve that is.