Did you try to reboot the computer?

Can you find the Firefox installation folder?

• /Applications/Firefox.app

Make sure Firefox gets installed properly.

Open the Firefox Disk Image file and drag the Firefox application to the Applications folder on your hard drive. You shouldn't double-click the Firefox application to run it from the Disk Image, but instead drag it out of the DMG folder.

• http://kb.mozillazine.org//Installing_Firefox#Mac_OS_X
• https://support.mozilla.org/kb//Installing+Firefox+on+Mac

Try to do a clean reinstall and download the full version and trash the currently installed Firefox application..

Download a new copy of the Firefox application and save the Disk Image file to the desktop

• Firefox 50.1.0: *https://www.mozilla.org/en-US/firefox/all/

• Trash the currently installed Firefox application (open the Applications folder in the Finder and drag the Firefox application to the Trash) to do a clean reinstall
• Install the new version that you have downloaded
• https://support.mozilla.org/kb/Installing+Firefox+on+Mac

Your personal data like bookmarks is stored in the Firefox profile folder, so you won't lose personal data when you uninstall and reinstall or update Firefox, but make sure NOT to remove personal data when you uninstall Firefox as that will remove all Firefox profile folders and you lose your personal data.

Failing to understand how an application can be running in the background, I used El Capitan Cache Cleaner to clean cache, and downloaded a fresh dmg of Firefox 50.1. Replacing the application from the disc image, and a restart resolved the issue. The dialog warned me the copy on my mac was newer than the fresh dmg application. But it has resolved the hiding issue. Thanks Mozilla volunteers.

The other main cause of the hiding Firefox, I suspect, was the recent install of Adobe Flash Player. When I chose to uninstall this program it did observe and allow me to quit Firefox and Safari in one window to remove itself. So perhaps this Flash Player is the majority of the problem.