The "problem" is probably because of the confusion on how to classify your contributions by means of payroll deduction.
On your W-2 in box 12 with a code of "W", there is the "employer contribution". This amount consists of both your employer's contributions AND your contributions to the HSA by means of a payroll deduction plan.
This code W amount is removed by your employer from Wages in boxes 1, 3, and 5 on your W-2. This why you don't see you payroll deduction amounts show up on line 25 or the tax return, because they were never included in your income in the first place.
Thus, line 2 on the 8889 should NOT contain any amounts that appeared on your W-2, but only contributions you made outside of your employer (what are called "personal" contributions). Line 9 should contain the amount from your W-2.
