Hi again, @AydenHumphries ...
This is pretty strange. I just tried creating a new assignment in my own sandbox course where I only allowed my dummy student to attach a *.zip file to the assignment. Then, when I masqueraded as the dummy student, I attached a *.zip file that had four *.stl files (3D printing files) in it. When I looked at the submission as a student, I was able to download it and unzip the files as expected. When I returned to my own instructor view, I was also able to download and unzip the file normally without it being empty as you've described.
I'd recommend contacting the Canvas Support folks using the information I provided earlier. You might even try reaching out to your school's Canvas administrators or someone from their Online Learning / eLearning / Distance Education team. They may be able to provide some additional insights for you.
Good luck, and keep us posted!!!