It is best to maintain close contact with your contractor so he will know immediately when you are not happy with something. The best way to do this is to schedule a daily or weekly meeting with your contractor or lead carpenter. To make these daily and weekly meetings productive, take a close look at each day's work after the work crews have left for the night. If something is wrong, by all means bring it to your contractor's attention as quickly as possible. It's better to deal with job site surprises calmly.
Few mistakes are intentional, they're often the result of a mix-up in communication by the workers.
Normally, that is not a problem as long as the contractor hasn't started on that part of the project yet. Such changes or additions will cost you less if you mention them early in the job.