'Substandard' might have been the wrong word. But oftentimes two fabrics that appear to be the same (the same design) may not be.
They may be printed on different quality greige goods (the unprinted cloth).
They may be the first run of the fabric (strikeoffs) and don't have all the finishing processes added (which help prevent shrinking or fading).
They may have a slight inconsistency in the printing and can't be sold as first quality (i.e. the middle of a flower is printed in the wrong place or the wrong color).
Why does Joann's charge the same price? Perhaps because they run a lot of sales or have 40% off coupons and they still need to make a profit??