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Neither of us ever made any direct contributions to our HSA accounts. All contributions were through our respective employers. I cannot explain the discrepancy between what was reported on my spouse's W-2 ($2,1,25.05) versus what was actually contributed via the HSA transaction history ($2,464.72). It appears to be a mistake by the employer. I have attached a screenshot of the HSA contribution transactions, it very clearly adds up to $2,464.72, all categorized as 2018 employer contributions. 

Regarding our 8889 details, see below:

Your 8889 - Lines 2 + 9 = $3450.00

Your 8889 - line 5 minus line 6 = $3450.00 

Her 8889 - Lines 2 + 9 = $2464.72

Her 8889 - line 5 minus line 6 =  $3450.00