In case anyone encountered problem with Joomla media manager when uploading new files and creating subfolders (nested folders) here is a link to quick solution.

This is a bug in Joomla! 3.3 and this should fix the problem you are having:

github.com/joomla/joomla-cms/pull/3575/files

Issue persisted whenever you tried to create new nested folder, instead Joomla! would create folder in main /images directory. Additionally problem with uploading media files (images. videos, etc) occured whenever you would try to upload them to the subfolder, and again in this scenario Joomla! would upload those images into main image directory. Above link points you to a solution which should fix the bug.