Category page showing posts from all categories

That happens because you are overwriting the query with you $args, If you want to modify it and not overwrite it then use this format:

//get the $query_string in to your $args array
global $query_string;
parse_str( $query_string, $args );
//modify whatever you want
$args['post_type'] = 'post';
$args['posts_per_page'] = 5;
$args['orderby'] = 'comment_count';
query_posts($args);