How to clean the html output of textfield using CKeditor?
I have run into this, I'm not sure if there is a configuration value to avoid this. I usually end up installing Empty Paragraph Killer.


  Empty paragraph killer is a filter module, helpful on sites which use
  WYSIWYG editors.
  
  People often hit the return key twice at the end of a paragraph. Most,
  if not all site layouts manage the paragraph spacing, so the extra
  empty paragraphs created can detract from the look and feel of a site.
  This module filters out the empty paragraphs of all user-entered data
  on a site. It does so by following the fundamental Drupal way -
  non-destructively.