Quite frequently, in the written specifications, there will be a disclaimer that usually puts the burden of code problems squarely on the contractor. Also, there will be other language involved in an attempt to relieve the engineer/architect of any responsibility for his omissions.
It may be time to consult an attorney specializing in construction contracts. Otherwise, you could make the changes & if you don't get paid, try placing a lien on the property.
By the way, weren't the plans submitted for review by the AHJ prior to construction? Seems to me the AHJ dropped the ball if there was a plan review.
Few things are harder to put up with than the annoyance of a good example.