I can see shortcodes in my excerpts - how do I use custom excerpts?

Excerpts do not support shortcodes or HTML, they just display unformatted text. By default excerpts will strip all the HTML tags but you'll see raw shortcodes so you'll need to use custom excerpts to remove these. To do this edit the desired post or page, click the Screen Options button in the top right corner and check Excerpt. Now scroll down to Excerpt panel to add your custom excerpt.