She isn't lying. It could easily take two hours of labor to cut, shape, and smooth that piece. Add in your tooling, insurance, and other overhead and 50 bucks is pretty reasonable. Not to mention the material probably cost them 10 bucks a foot. Even though it's waste, it still cost them in the beginning.
Just for information's sake. Most people don't realize how much work is involved with smoothing out the cuts. When you cut a piece out the edges are rough. Then you have to round off the corners with a grinder. Run some stone wheels of different grits to flatten the cuts (the blade will drift sometimes) and smooth off the rough edges. Then you run thru at least 6 different polishing pads.
Basically, anytime you fabricate or install granite, every bit of it sucks. It is dirty nasty work.
The only part that doesn't suck is walking away with a satisfied customer. That's it, nothing else.