There are two ways to make HSA contributions: through your employer and directly to your HSA.
If you make contributions to your HSA through your employer (whether it is your employer's contribution or yours through payroll deduction), this appears as an amount with the code of "W" in box 12 on your W-2.
When your employer prints your W-2, he/she removes the code W amount from Wages in boxes 1, 3, and 5 on your W-2. This is why you don't see a deduction on your tax return for these contributions - because they were never in your income in the first place.
If, on the other hand, you made contributions to your HSA directly to the HSA custodian (not through your employer), then these contributions appear on line 12 on Schedule 1 (1040) as an adjustment (reduction) to adjusted gross income (AGI). You enter these contributions on the screen with the heading "Let's enter [name]'s HSA contributions" on the second line where it says "personally" (see screenshot below).
You will see under Deductions & Credits ONLY the line 12 amount, not the W-2 amount. This is what is happening in your case.
Either you contributed to your HSA differently in 2018 than you did in 2017, or one of the two years is wrong and will need to be fixed.
[Edited 4/1/2020 2:06 pm CDT - updated for 2019]
