One way the math would work is if you entered the $5000 as an independent contribution in the HSA interview. Workplace contributions should only be entered via the W-2. If you had $5000 workplace, and entered the $5000 again in the main interview, you would have $10,000 total which is a $2250 excess.
On form 8889, Line 2 should be blank or zero. Line 4 should be blank or zero (Archer MSAs are uncommon). The employer contribution from your W-2 should be on line 9. If you have an entry on line 2, that means you double-entered your employer contribution as if it was an independent, after-tax contribution.
