Icons not showing properly in Yosemite's Safari favourites bar

Solution 1:

These are two different icons:

• the ones in the sidebar are Favicons icons
• the one in the favourites are Apple specific (only shown by Safari) and called Web Clips (or Apple Touch Icons)

They are both downloaded from the site but can be different.

For example IMDB specifies

• http://ia.media-imdb.com/images/G/01/imdb/images/favicon-2165806970.CB379387995.ico as Favicon and

• http://ia.media-imdb.com/images/G/01/imdb/images/mobile/apple-touch-icon-web-76x76-53536248.CB361295462.png as Web Clip

From the comments: you can add a clip following these instructions:

To create a webclip, go to the site you want and tap the box-and-arrow icon used to create bookmarks. In the menu that pops up, tap the Add to Home Screen option. Edit the name of the webclip and tap Add. You'll then be taken to your home screen and shown the webclip. Tap it to go to that site.

Solution 2:

No, Apple Touch Icons are uploaded alongside the HTML files on the website, usually in the root folder. Safari just pulls them from here if they exist. It is up to the site owner to add them.