The fact that this clear CD was in your CD case is probably a mistake. CD's start out clear and are only playable when the silvering is added (this reflects the laser beam back to be read). Sometimes damaged clear CD relects are placed on the top or bottom of a stack of good CD's to protect them from scratches etc. The machine probably accidentally picked one of these up and packed it with your good CD. There's some dtails about the CD manufacturing process here.
http://www.acmecd.com/manprocess.html