Hi,
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:
![Image Text](http://content.screencast.com/users/DavidTK/folders/Jing/media/7dbf62ed-9009-4ef9-ac9c-347d600fe0cb/2016-04-11_0937.png)
You can just select the Dancing Goat site as Web Template when creating a new Site using Wizard.
![Image Text](http://content.screencast.com/users/DavidTK/folders/Jing/media/43942e09-fa4e-4de0-8a4a-46a1b875805b/2016-04-11_0943.png)
Greets,
David