@Anonymous, I agree with you that box 12 should include only the contributions your employer made, since they're calling it “Employer Contributions”! But someone at the IRS (who wasn’t being as sensible as you are) decided to call it that even though it includes amounts deducted “pre-tax” (in a cafeteria plan) from the employee’s check (see the instructions for Form 8889 here).
It does make sense that the two different kinds of contributions are treated the same. As Critter-3 and others said earlier in this thread, they’re both amounts which the employer is considered to have paid to you, which weren’t taxed because they went to the HSA instead of directly to you. So they both go toward your maximum contribution for the year, and no distinction is made between them in the event of excess contributions or for other purposes...
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