This effect usually occurs when two geometries coincide in the exact same place. It looks like you might be generating the gray and blue faces, while you actually only want the blue.
Here is a short rule that will show that effect:
@StartRule
Lot -->
extrude(10)
ColorItGray
ColorItBlue
ColorItGray -->color(0.5,0.5,0.5) X.
ColorItBlue -->split(z){1: color(0,0,1) X.}*
During the Lot rule, it is sending the same geometry to two different rules, each of which create geometry in the same space, which gives the visual effect you are seeing.
Does this help? If not, if you can post the CGA here, we could look closer.
Chris
