You're right this shouldn't be the case. This happens when your update the layout (so the html) of a Page Template and remove webpart zones (but you leave configured webparts in them). They will end up as orphans the way your screenshot displays.
Since Kentico version 8 they also provided a more 'realistic' demo site also including eCommerce. So you probably want to have a look at the Dancing Goat site:
You can just select the Dancing Goat site as Web Template when creating a new Site using Wizard.