How to use `the_content` filter properly? [closed]

Question

I have a plugin that filters a particular page, and another plugin(a widget actually) that uses WP_Query to display a number of posts list. The problem is when I am on that particular page that is filtered, the widget that displays a list of posts, gets affected, and displays the content of that filtered page. So I get bunch of cloned contents all over the page, in the content area and in the sidebar(where the widgets reside). How do I filter the the_content so this won't happen, or make the widget so it will function as expected?

the filter code:

add_filter('the_content', 'content');
function content($content) {
    return $content . get_custom_content();
}

the query code:

$second_query = new WP_Query( array(
                        'post_type' => "$post_type",
                        'post_status' => 'publish'
                    ) ); 
// The Loop
if ($second_query->have_posts()) :
    while( $second_query->have_posts() ) : $second_query->the_post();
        $content .= '<span class="permalink"><a href="' .get_permalink(). '">' . get_the_title($post->ID) . '</a></span>';
        $content .= '<p>' . get_the_excerpt() . '</p>';
    endwhile; else :
          $content = '<p>No ' . $options['post_type'] . 's found.</p>';
endif;
wp_reset_postdata();

$title = "<h3>" . $options['title'] . "</h3>";   
echo $before_widget.$title.$content.$after_widget;

SOLUTION:

So came to a conclusion that it's a known issue with the_content messing up with WP_Query. It's discussed here: http://core.trac.wordpress.org/ticket/18561#comment:48

My solution is I installed a filter in the template and filter it instead of the 'the_content':

$below_post_content = '';
echo apply_filters('custom_filter', $below_post_content);

Note that action hook won't work in this case. I don't know why.