This question is quite vague, but sounds like a plugin-specific issue. No true shortcode (i.e. your plugin) should be doing this, and the way the theme implements the raw shortcode is quite common (which is not a true shortcode either). So, I’d start by contacting the author of the plugin. I’m sure if you’re experiencing this issue, many others are, as well, and so the plugin author will probably have an answer for you.