Yeah, it appears I wasn't duplicating them when they were completely aligned. I've zoomed in much more to make sure everything is exact. As a test, I have two squares snapped next to each other and zoomed in. When I remove the grid I can still see a faint line in between the squares. I'm not sure if this is to indicate they're separate layers or if the gap will show when I export the final object. The background is blue, the squares are red.
Also, is it possible to use my mouse/trackpad to select multiple squares at once? I know I can marquee select them but I'd like to do something like hold "command" and select multiple layers on my artboard NOT select from the layers panel.