I'm trying to fill all of the squares with a black fill color but only the corners are getting filled. I've been using shift + x to toggle the stroke color to the fill color.
It's not clear how the grid is constructed. If you can, please post another screenshot with all selected and the Layers panel in view.
the live paint bucket did the trick but this was my layers panel
Yes, this is exactly what I told about: each element is a line, no objects to fill. Live Paint Bucket is the best tool in this case.
Try and use Live paint to fill it.
Looks like you have drawn corners by 2 lines each one (horyzontal+vertical) and many separate short lines between the grid points. So you don't have any closed objects. Corners are filled by connecting the path endpoints with the shortest way (diagonal line), but other grid elements are just lines, not fillable at all.
So now you can only do what Monika suggests: select all the grid cells and use the Live Paint Bucket tool (it is under the same button as Shape Builder tool)