I predict a battle and I hope you will persevere thru the process to win this. Its despicable that someone would even try to represent this as acceptable. Its worth doing some basic research if your state has builder's licensing (they may not) as there should be an organized process to dispute this, and no arbitrator is going to side with this as being work that should be paid-for in same condition.
A tool you might use if you need it is to bother the person incessantly. In their world, time is money, and the more time they spend on your problem, the less they can devote elsewhere. They might block your calls or refuse to take them but psychologically they know its you who is calling. I'd leave voice mails and send letters. Obviously if a legal process or an organized process with the state starts then you can't do this. Part of their strategy is to see if you tire out first, but if you can become a constant PITA, the might cave in just to get you to "go away". Squeaky wheel gets the grease phenomenon.