Why does the HSA Employer contribution amount differ from what I actually received in my HSA account?

You should definitely contact your employer about the discrepancy- sometimes there is a lag in reporting due to the dates (for example if there is a Cafeteria Plan with a different benefit year) , but the HSA contributions should align with the calendar year.

I think that amount on box 12 Code W. also includes your /employee's contribution to HSA through your employer.