The 5498-SA doesn't list the "employer contributions" anywhere; it lists total contributions. Perhaps you meant the same thing, that all of your contributions were through the employer. But if you made direct contributions, it would show up on the 5498-SA, too.
But I am now concerned on this discrepancy. Why did her employer report $2,125.05 on her W-2? What did you do with the $2,464.72? What is the difference? Did she make a direct contribution to the HSA outside of her employer?
What did you enter for the following:
Your 8889 - Lines 2 + 9
Your 8889 - line 5 minus line 6
Her 8889 - Lines 2 + 9
Her 8889 - line 5 minus line 6
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