Employer contributions deducted from quoted salary—is this normal?
To deduct employer contributions from the salary as well as employee contributions would be highly unusual, I believe. (If it were the norm, then there would be no need for a terminological distinction between employer and employee contributions.)

EDIT: Here is my guess about what happened (purely speculation).  Perhaps there are contributions that are classified as "employer contributions" for tax purposes, and the university requires these contributions to be made for postdocs as well as regular employees but only makes the contributions for regular employees, so for postdocs the money has to come out of a grant instead.  This situation has the potential to be confusing, so perhaps your advisor simply forgot about this until you reminded him, at which point he realized that he made a mistake.

In any case, the question you asked him in your e-mail was completely reasonable.