I took a look at your project and there are a bunch of problems, starting with the AI file. The layers are NOT pixel perfect:

The color space is not correct for video, but more importantly, if you turn in Pixel Preview it is clear that the fill pattern was not created with Snap to pixel turned on so it doesn't line up. These are the lines you see in AE.
But wait, there are more problems:

This is actually the first thing that I saw that tells me that the artwork was not properly prepared for video. You should never have vector artwork that is an odd number of pixels high or wide. It is difficult to get horizontal or vertical edges lined up with the pixel grid. You either have to adjust the anchor point or the position, scale throws interpretation errors and it's just not a good idea, ever.
There are also some basic problems with the composition settings:

I won't go into detail but you should never rely on the composition background color to give you a colored background when you render.
I took a look at all of the comps. They all have issues but Comp 2 shows the most obvious problems:

All of the problems I see in the comps can be reduced or completely eliminated by properly preparing the artwork for video. There is no bug. The problem is entirely user error. Fix the AI files and you fix the problem as long as you follow the rules and keep the edges lined up with the pixel grid when the graphics are at rest. When they are moving, motion blur and speed will hide the aliasing problems that cause the patterns to appear so you won't have to worry about them, you'll just have to hide them.