Some pasta machines do that. I THINK it has to do with minute flaws in the scraper blades. You can order replacement scraper blades from Mona Kissel (http://www.monakissel.com/toolspasta.html)
I really suggest sending them your pasta machine and having them modify it for easy cleaning, too. It's $25 plus shipping both ways (another $25 more or less), and WELL worth it!
To solve your problem at this time, try laying your ridged sheet down crossways and lightly brayering or hand rolling over it. No real pressure, just let the weight of the roller smooth the surface. Or cover with a sheet of paper and burnish with a credit card, back of a spoon, or your fingers. Be careful because you can "dent" the clay with too much pressure.