I work in a LQS, and we see it occasionally. But not that often. There have been a couple lines of fabric that came with an information page, telling us to inform our customers that the fabric was likely to bleed. Gee's Bend hand dye was one. And we have a 54" wide chambray collection that we warn the customers about.
If I'm measuring out yardage, I try to spot any imperfections, and point them out to the customer. If we find anything, we can give them 30% off, or cut a new piece. It's not a happy day when an imperfection is smack dab in the center of a big piece! But sometimes we can work around it.
Woven (yarn dyed or homespun) fabrics have imperfections. It's just a fact that we have to live with. It's what gives it character.
Some white on white fabrics have bits of other colored threads in them occasionally. It's like other fabric lint was in the air when the WOW was being woven, and it got woven in. Sometimes they can be picked out. Those fabrics are a lower price for that reason.