Using apply_filters(‘the_content’, $custom_query->post_content) alters output

the_content filter takes only one parameter – $content, so you can’t check what post this $content comes from.

So if the plugin Team performs incorrect checks (it can for example use is_singular( <POST_TYPE> )), then it will modify all contents printed on single team member page.

You’ll have to check what functions are assigned to the_content hook and check what exactly are they doing…