Hi Zen! Sorry for the frustration, we could probably show a "warning" for this in the future. What's happening is, you've pushed two verts (top and bottom) into the exact same position, which creates an impossible surface, and can't be rendered properly. If that doesn't make sense- when you pull those top verts down, and they land exactly on the bottom verts, they bottom ones aren't automatically deleted.
Why aren't they auto-deleted? Well, we've generally tried to not "guess" what the user wants, and do hidden, automatic stuff. So, you'll need to merge those overlaid vertices- try using "Collapse" or "Weld" (make sure "Select Hidden" is on when drag-selecting, to get both vertices).
Hope that helps!