Random scale issues on pixel art

Question

I'm creating pixel art animations for an LED presentation. The video size and comp sizes are 96 pixels x 64 pixels. I created the pixel art in Illustrator at the same size. I started out by creating a 96x64 grid and then using the live paint to fill in each box to create the artwork.
In After Effects I start doing my animation but sometimes when something is scaled down, issues start occurring. For example, I have 2 black squares as eyes. Both are 1x1 pixels or a 1x1 box in illustrator. Once they are scaled in AE, one eye may be bigger than the other. Is there some sort of interpolation issue happening? One solution I have tried using is only using draft mode. That works the majority of the time to keep everything looking very pixelated except for when the random scale issues occur.

Answer 1

To be more clear of what I am trying to do. I am creating an animation for a Christmas LED display. I created 20-50 pixel art assets at the 96x64 size. They may not have all been to the final scale I wanted them to be in my animation. I brought my assets into AE and began doing my thing by animating. The original goal was to create Christmas animations that were a little more advanced than some pixel art simply moving position across the screen and to try and create a story based on the songs that were playing.
In my particular example where I am having an issue. I created frosty the snowman and the animation is him moving his arm and tipping his top hat. I'm not animating his eyes at all which are just black squares. Although the eyes are the ones creating the issues. One eye is bigger than the other. When I look at the original Illustrator asset, the eyes are the same size. Currently, everything is 100% to scale and draft mode in enabled. If it weren't for the eyes, it would look just like the illustrator artwork. When draft mode is disabled, that is when edges are no longer crisp and there is some slight feathering around all of the edges.