I have heard that manufacturers use the same prints on different "greige", meaning different qualities of underlying fabric. They also will use a different series of finishes on fabric -- a more complex series of finishes on the higher priced fabric, and fewer finishes on the lower-priced fabric. This was the major reason why quilters were advised to buy from LQS instead of discount places.
I have been able to notice differences when I have found the same fabric at two different places, such as LQS and Walmart. However, there are also times when I haven't been able to detect any difference between the two fabrics. That makes me think that sometimes the discount store has simply gotten a "deal" on a better fabric but that sometimes it really is a less desirable version of the fabric. I haven't noticed any problems with LQS fabrics, so assume they never buy the lower quality version of a print.