It sounds like to me that he made a mistake in his math and when it was pointed out to him, became defensive. And more than likely he probably feels that he should have a better job somewhere else than working in a LQS cutting fabric.
All that said, poor service from store employees is a MAJOR pet peeve of mine and I have no problem with making that known when it occurs. If they want my $, then they sure had better not treat me with contempt and disdain.
But, there are right ways of dealing with the issue, and I think you did the right thing in pointing it out to him. The fact that he doesn't "get it" means you simply need to politely take the matter up with the owner. I would write a polite letter, stating the facts of the cuts, and then saying that a mistake has obviously been made which you tried to rectify with the employeee to avail. I wouldn't say anything ugly about the employee, however tempting that might be, but you could say that in trying to resolve the matter with the employee that they were unable to understand the mathmatics of the mistake. I think with this approach that the owner will refund you what you are due, and also appologize for the oaf of a son.