Previously, the logic that added the active class to the <li> element (not the link) was located in directly in the theme function: bootstrap_menu_link().
In an effort to conform with best practices, this has been moved to the preprocess function bootstrap_preprocess_menu_link().
If your sub-theme has overridden this theme function, but didn't actually alter any of the active class logic, then simply remove that logic from the theme function.
If your sub-theme has overridden this theme function and also altered the active class logic, you will need to move this logic into a new preprocess function in your own theme. Keep in mind that you will now also have to remove any active class set by bootstrap_preprocess_menu_link() if it differs from your own logic. Preprocess functions are accumulative, not overridden by sub-themes.