the contributions are not reported on the 1099-SA form. it only reports amounts withdrawn from the HSA. for HSA contributions you would get from 5498-SA. if they were made from payroll deductions that would be the amount in box 12 code W on your w-2 which flows to line 9 of form 8889. do not duplicate them on line 2 of form 8889. that line is only for contributions you made directly to the HSA.
the 5498-sa the IRS got must match the totals on lines 2 and 9 on the 8889
