Dock and Menu Bar Disappear in OS X El Capitan When in App Window
It turns out this is a bug with Firefox. These instructions I found fixed the issue.


  
  In Finder right click on the Firefox app and select “Show Package Contents”
  Navigate to Contents and open “Info.plist” in TextEdit.
  In this file, near the top, there should be a piece of text that says &lt; dict >, underneath this add the following making sure all of the
  text is present.

&lt;key&gt;LSUIPresentationMode&lt;/key&gt;
&lt;integer&gt;0&lt;/integer&gt;

  Save that file
  Restart Firefox
  Happy browsing again
  


src: https://discussions.apple.com/thread/3096551?tstart=0