Related documentation: WPSSO Debugging and Problem Solving
WordPress allows plugins and themes to hook into hundreds of different filters to manage content, some of which are used by WordPress to expand shortcodes, for example. WordPress generally calls a filter (like ‘the_content’) once to expand text for a given post within the loop or a single webpage. As a consequence, some authors mistakenly assume that a filter they have created will only be executed once for a given post, and only within the webpage body or specific area. WordPress filters are available to any theme or plugin that needs to expand text (title, excerpt, content, etc.), and in any context (header, loop, widget, admin, etc.). WPSSO Core uses ‘the_content’ filter to locate media elements within the content, and to provide complete and accurate description meta tags.
See the “Is your filter going to break the layout?” post on the Make WordPress Plugins blog for additional information on the use (and common misuse) of ‘the_content’ filter by developers.
Under the SSO > Advanced Settings > Plugin Settings > Integration tab, you can uncheck the “Use Filtered Content” and “Use Filtered Excerpt” to see if your problem is related to a WordPress filter hook. If unchecking these options fixes your problem, you should determine which plugin/theme is at fault and report the issue with the plugin/theme author. Using the WordPress <span class="spanvar">apply_filters()</span> function should not break a theme and/or plugin.
If you disable the content filter, and your Post / Page content relies upon shortcodes for its text, then you may find that WPSSO Core cannot create accurate description meta tags (or any description text at all). WPSSO Core looks for a custom description and excerpt before falling back to using the content text. In the case where content filters are disabled, and the content uses shortcodes for its text, then you may have to enter an excerpt and/or custom description for those Posts / Pages.
Since WPSSO Core uses the custom description and/or post excerpt before falling back the content, using a custom description and/or excerpt for a few Posts/Pages could be another alternative to disabling the content filter for the whole website.