You did correctly. Your supervisor was in error.
HOWEVER -- the way you described it in your opening post, it sounded like the engineer designed one side of the foundation and then just added a note to do the other three sides "per code." That, IMHO, is NOT appropriate. The foundation plan should show all four (or six, or eight, or however many) sides and should show exactly how all sides are to be built. If the details for all the other sides don't show anything more than the prescriptive design from the IRC, that's fine -- but the drawings should show how each wall is to be constructed. Notes such as "per code" are never acceptable, and have never been acceptable.
The contractor in the field may know more than any of us about the code, but there should not be any reason for a contractor to open a code book on the site. There's a reason why those pieces of paper are called "construction documents." It's the designer's job to follow the code. It's the contractor's job to build what's shown on the drawings.