If you told the Foundation contractor what height to place the foundation, you take responsibility. If you had a plan that told him what height to place the foundation, you take responsibility. If you "left" it up to him the determine heights, and it was incorrect, he bares the responsibility. If the excavating contractor cut the hole to deep, and the General contractor did not catch it, he bares responsibility.
It is no up to the foundation contractor to "know" what code is in this regards. It is up to you, the acting contractor, to know this and determine what heights the wall should be placed.
As far as fixing it, you can add to the top of the wall. I am guessing you will need it engineered to do so. I would not remove the wall though.