I updated Wygwam to the most recent version (3.3.3) and now the icons in the toolbar all got messed up. I tried re-uploading the themes folder, and emptying the cache, but no luck so far.
EE version? And do you have a custom theme? What accessories do you have installed? They can inject CSS/JS into your CP pages.
Using Chrome or Firefox, right click on one of the mal-positioned icons, and look at the CSS rulesets applied to the icon. See what CSS asset file is messing with your icon elements.