Become a MacRumors Supporter for $50/year with no ads, ability to filter front page stories, and private forums.
It's a Safari bug. I had this happen a couple months back. Here's what I did to fix it:

  1. Close Safari.
  2. Open your terminal.
  3. Run this command:
    Bash:
    open ~/Library/Safari/Favicon\ Cache
  4. Finder will open. Delete the contents of the folder.
  5. Browse sites and see that it redownloads the favicons and stores them correctly this time.
 
Register on MacRumors! This sidebar will go away, and you'll see fewer ads.