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I cannot post the Shader code itself, but I was wondering if there is some common problem that occurs for Shaders where this would happen.
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Looks to me you're discarding pixels in a pixel shader, or having multiple passes where you end up with Z buffer fighting due to previous pass overlay. Sorry for the vague answer but you don't provide much information. :) Are you messing around with the mesh in any way? Just considering there might be some issues if not all data channels are populated... It looks linked with vertex data from the shapes.
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Your answer
Looks like z fighting. Check for almost-coplanar polygons, and also make sure your camera near/far clip planes are reasonably tight around the geometric extent of your world.
It is almost impossible to guess what you are doing just from the picture, maybe transparency, maybe the depth buffer? You will probably have to give some shader code.