I am not quite able to reproduce this - perhaps I am missing a step.

If I control-click the extension in the menu I don't get the contextual menu. Instead I get the extension's bubble. But sometimes if I dismiss the bubble the icon is left highlighted.

I also found that if I place an extension in the menu and control-click it it comes out and I get its contextual menu. If I choose to keep it in the toolbar it stays there but also remains highlighted.

I've been able to repro and written a fix while investigating another bug.  I'll snag this one from you, if that's okay. :)

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/e3a55f8fe3980f561aaba28e1a593d7ad020653b

commit e3a55f8fe3980f561aaba28e1a593d7ad020653b
Author: rdevlin.cronin <rdevlin.cronin@chromium.org>
Date: Thu Apr 14 19:16:40 2016

[Extensions UI Mac] Fix a bug with popped out actions' highlighted state

Fix a bug where popped out actions wouldn't clear their highlighted
state and add a couple of tests to protect against regression.

BUG= 601249 

Review URL: https://codereview.chromium.org/1888133002

Cr-Commit-Position: refs/heads/master@{#387389}

[modify] https://crrev.com/e3a55f8fe3980f561aaba28e1a593d7ad020653b/chrome/browser/ui/cocoa/extensions/browser_action_button.h
[modify] https://crrev.com/e3a55f8fe3980f561aaba28e1a593d7ad020653b/chrome/browser/ui/cocoa/extensions/browser_action_button.mm
[modify] https://crrev.com/e3a55f8fe3980f561aaba28e1a593d7ad020653b/chrome/browser/ui/cocoa/extensions/browser_action_button_interactive_uitest.mm

This should be fixed (it no longer repros for me locally).  ainslie@, in a day or so when this is in Canary, can you verify?