I actually do not know where this error stems from, but here we go. I was attempting to encode an After Effects composition containing 5 video files with opacity changes only, but 2 of the video files always got encoded looking like this. I was trying to encode it into an MP4 file. Whenever I check the After Effects file, all of the videos are intact, but it still doesn't work for Media Encoder. I attempted encoding 4 times, and restarted both After Effects and Media Encoder to check if that helped.
I did try searching the forums, but because I'm not sure what keywords to search, I couldn't find a post that also had this error.