The 5498-SA will report on the total contributions to your HSA from all sources.
Your W-2 reports (in box 12 with a code of W) the sum of the amounts that your employer contributed and what you contributed by means of payroll deduction. It will not include any amounts you contributed directly to the HSA outside your employer (but the 5498-SA will).
Since the 5498-SA came from your HSA administrator, they are in the better position to know what amounts were actually contributed.
Compare the detail of your HSA account (probably available online) with your W-2 - if there are discrepancies that aren't explained above, you need to start investigating.
