Talk to a lawyer for a free consultation. A contract cannot require you to waive your rights. If they made such a costly mistake, it's unlikely it would hold up in small claims court. (You are smart, and you could probably file the small claims court paperwork yourself.) But before you do so, write a very formal letter, telling them that you have researched your legal options, you realize that their case will not stand up according to contract law, and you plan to file a claim in small claims court within 15 days of the date of the letter unless they resolve the issue satisfactorily.