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I am using Safari 9.0.3 on OS X 10.11.9 and have only recently noticed Safari displaying the wrong favicon for some websites.
In one instance, Safari uses the Facebook icon for Messenger despite the Messenger icon being used in the head section of the page source.
I tried deleting the WebpageIcons.db file from Safari's Library folder, and I have cleared Safari history and website data across all my devices.
The Facebook icon still loads.
Edit: To clarify, the proper Messenger.com icon appears in the bookmarks menu and the bookmarks editor window. However, the Facebook.com icon is used in the Smart Search Field.
Facebook's Messenger.com icon: