Question: For some reason I have two "elephant" icons from Evernote at the top right menu bar. Does anyone know if this is a bug in Evernote or how to remove the extra one?

**Additional Information:**
This problem is still seen after the following steps:

1. Completely wiping the drive on a Macbook Air
2. Installing Mountain Lion from scratch
3. Installing Evernote from the Mac App Store

After installing from the Mac App Store two elephant icons will appear on the menubar.

Answer: 
I had the same problem and resolved it by going to:

System Preferences > Users & Groups > Login Items [for my user]

Then I deleted the EvernoteHelper (select and press the "-" button).

Finally, I unchecked all of the tickboxes under Evernote Helper in Evernote's settings itself, and then re-checked them. Rebooted and only one elephant. Happy days :)
Sounds weird. Have you tried to relaunch Finder? Apple->Force Quit->Finder and click relaunch.