It looks like you're extruding the logo by taking a bunch of layers, stacking them in z-space, and spinning that whole precomp with collapse transformations on.
Think of a layer in After Effects's Classic 3D renderer like a piece of paper. It's essentially 2D. It's got width and height, but no depth. The renderer lets you manipulate these 2D layers in 3D space, so we often refer to this as 2.5D. However, when you're pointing a layer's edge directly at the camera, you can see that it's infinitely thin, and in your project on the frames you've marked "Problem," that's exactly what's happening: the stack of layers in your extruded logo are pointing their edges straight at the camera and you can see right through the gaps.