I can't imagine someone doing that and getting away ith it.
I have a second job in a fabric store, and we have a 20 cm minimum. The only rule we have is that we will not make several cuts of the same fabric, like if the customer wants 6 strips of 30cm of the same fabric, we will cut one 1.8 m chunk, and the customer is responsable for the rest, we're not going to do their work for them.
I had a lady come in last week and buy 40cm of each of the colours in our broadcloth (26 colours, I think), and when I was almost done, she decided she didn't have enough and asked for another 40cm cut of each, so I basically cut 52 pieces of fabric for her. There were people in line, I didn't make a stink about it, didn't charge extra because there were so many, and small pieces at that. She was charged the price on the bolt and that was that.
I think the guy who served you was way out of line, and I would not hesitate to politely bring it to the owner's attention if I were in your place.
Mistakes happen, but he should have owned up to it, at least offered you a 2/3 of some other fabric.
Also, I meant to ask, if you had two fabrics that were cheaper than the rest, wouldn't he have added them up seperately? Did he charge you an extra 2/3 of regular priced fabric, or discounted fabric? Not that it makes a difference, but his argument doesn't hold water.