Coloring a Die

Good evening, Blender Artists! I’m new to Blender and I have a problem with coloring a 6-sided die. I was following this tutorial - I followed everything using the second method with one exception: instead of moving the dots in as a whole, I moved just the central point, as in the first method. It looked fine, but when I went to color the holes black, some of them got colored on the outsides. (only a few seemingly random ones did this). Attached is what one side of the cube looked like.