Joomla uses a specific folder for images used in Articles and other content items.

The folder is at

Joomla root/images/stories/

The stories folder is where content images start.

User created folders can be nested within the stories folder. 

The level above contains system images that should not be deleted.

When uploading an image using a third party text editor such as JCE the stories folder becomes the upload root and the images folder is ignored.

If you have many images to upload it's faster to FTP to the stories folder than to use the Media Manager.

The stories folder is also used by third party extensions to store media such as audio and video files.

You might wonder why the stories folder isn't named articles. Many third party extensions depend on this naming and would fail if the name was changed.