As a rule of thumb you have to allow 10% on average for waste, it would be in the flooring companys best interest to have sent some extra material so they would not have to stop the job and have guys standing around waiting for the worker to go get more materials if they ran short.
Since you were being charged by the sq. foot then the left over material belonged to the flooring company not you, unless you asked for it and paided for it.
Keep in mind we were not there so this may or may not be true.
When I show up to build, lets say a deck. I always bring my boxes of joist hangers I have laying around and keep them in a differant area then the ones the customer paid for just in case I need them instead of having to drive an hour to pick the one up Im short.
Time and time agin they think I'm stealing something when they see me leaving with them. Even though even if they were there's they had 0 use for them.
The worst one wanted me to go back and count every hanger, every bolt and nail I used, even though the deck was being built for one set price.