Users expect listings of content types. We provide users with listings for taxonomy terms, menus, blocks, content types, and many other things. However, we do not provide users with listings for things like Articles and Pages.
When setting up the menu items, users add a menu item to a menu, then click the Preview button. They then really expected the menu item to show up in the menus during the preview.
User expected to know where content would show up while adding it - i.e., didn't want to add something and sort out navigation to it later. This was an expectation from other CMSes - i.e. browse to a folder and add content to it.
By default, page content is 'orphaned' after creation. Users cannot find it (outside of admin/content/node - which isn't part of 'the site'). This also happens with new content types.
When placing items in the Main menu (with the current hide the Navigation patch), users expect that the menu item will appear in the only menu they see, the Navigation menu. Users don't know where this new menu will appear.
User expected "Content" to be the first item under "Content management", but instead "Comments" were first, even though Content was much more important.