There is no difference between the favicon / small logo (the one which is used e.g. in the Achievements dialog) of Web Applications and Web Applications Meta:
(click to enlarge; the top one is meta, the bottom one the main site)
Meta icons are usually a grayscale-only variation of the main site icon, so I see why it is the way it is now. But can we please make one of them a few shades darker than the other?