as the owner, and you are untill the project is finished, stop the project, demand an anwser, was this approved by you? what were the resons he is given you for the changes? changes by a builder is usually because he has made a mistake, or he is trying to cover up items. if the change is a load bearing wall, then call the citys inforcement officer to see if there will be problems, if there is none there then stop project and allow him to correct unit at his cost. all materials & labor.
but if you make him pay for corrections, he will get you back before the project is over.