Dishonest roofers will do this at times. They get to charge more and
carry less weight.
You can have an old beat up shingle roof and it still won't leak when
the paper underneath is functional. The heavier paper is less apt to
get damaged while installing the roof and will make the roof more
serviceable. If you put an extra layer of shingles on later, which I
never would suggest, it helps there too.
I would not simply accept a refund of the tiny price difference on the
paper. The installation is what you paid for. I would pursue it if at
all possible for you to do so. I would spend money based on principle
here. That's just me.
My brother had his roof done by what was supposed to be a reputable
construction company. However, the crew leader was dishonest. They
thought they could take advantage of the situation as this brother
lacked the knowledge and physical capability of inspecting the work.
They ended up doing two complete tear offs before the work met the
contract and I signed off on it. Fortunately, the owner of the company
was reputable and did much work for the big insurance company. That
provided leverage you probably don't have in your case.