This is usually caused by another plugin or theme with built-in SEO functions Yoast's plugin disables many theme/plugin built-in SEO functions but it's not possible to do so always e.g. when non-standard WordPress hooks are used
Suggest switching to a default theme e.g. TwentyEleven for a short while - if the duplicate Meta tags disappear then it's the theme - which will need editing to remove the function if there's no option in theme settings.
If not the theme, then disable all other installed plugins and re-activate until the problem comes back.
Also - post a link to the site so we can see what's going on...