Help with Coin flip Glitch!

You will get co-plainer interference when you use the Advanced 3D rendering engine and have any bevil style and depth values added to the extruded layer. If you need the bevel, you must offset the surface layers by 1 pixel to fix the problem. This goes for both sides. Avoiding 3D layers that share the same plane is always a good idea. I often use expressions to offset the layers by one pixel in Z before moving them around. 

Before rotating the combination of layers, parent the front and back layers to the extruded layer, then add these expressions to the front and back layers' position properties. 

// front is child of middle layer
cntr = thisComp.layer(index +1);
ofst = cntr.position[2] - 1;
[0, 0, ofst]

// back is child of middle layer
cntr = thisComp.layer(index - 1);
extr = cntr.geometryOption.extrusionDepth + 1;
bevl = cntr.geometryOption.bevelDepth + 2;
posZ = cntr.position[2];
[0, 0, posZ + bevl + extr]

I have uploaded a project file for you to look at.