Adding additional content on post depending on post categories

The problem is that you are returning $content from within a conditional statement that could potentially resolve as false (and will, in the case of pages, because is_single() does not apply to pages).

Move your return to outside all “if” conditions to make sure that $content is always returned, regardless of whether it is filtered or not:

function my_category_content ( $content ) {
    global $post;
    if ( is_single() ) {
        if ( in_category( "", $post->ID ) ) {
            $content .= 'Only showing up on the categories named mini [product_category category="mini" limit="12" columns="4" orderby="date" order="desc"]';
        }
    }
    return $content;
} 
add_filter( 'the_content', 'my_category_content' );