This is usually caused by dirt or dust on the canvas that gets inked during printing and falls off afterwards. It seems to occur at the beginning or ends of rolls more frequently than in the middle.
It's possible to see the dust by holding a flashlight at a low angle across the canvas. The dust will usually be quite visible. We've had success cleaning it with a roller designed to clean prints before mounting or laminating. DryTac sells these.
If you need to do this, work on a very clean table and unroll the material face down first, clean the back, flip it, clean the front and reroll it.
As far as spotting goes, we've had some luck using acrylic paints and a very small spotting brush.
If this is done before the canvas is varnished, the spots dissapear.
Haven't found a permanent solution for water color papers (which often have the same dust problem. ). If it's a black area, a sharpie works.
Regards,
Marc Sitkin