Yes, it sounds like you need to amend.
The W-2 Box 12 Code W has all payroll contributions, from you, your employer, or both. The only place the payroll contributions should be entered is the W-2 section.
In the deduction section, this is correct that HSA contributions belong here, however you will only manually enter any contributions you personally made (not through your employer). You will only enter the amounts you directly contributed outside of paycheck withholding in the deduction section. Otherwise, it is double counting the amounts you contributed via your paycheck.
Both personal contributions and payroll contributions appear on the 5498-SA.
Here is some more information on filing amendments: How to File an Amended Tax Return with the IRS
