Append a GROUP BY clause to the current WP_Query SQL clause for the search.

functions.php

<?php
/**
 * Do not include php tags
 */ 

add_filter( 'posts_groupby', 'custom_posts_groupby', 10, 2 );
/**
 * Callback for WordPress 'posts_groupby' filter.
 * 
 * Set the GROUP BY clause to post IDs.
 * 
 * @global $wpdb
 * @see https://codex.wordpress.org/Class_Reference/wpdb
 * 
 * @param  string   $groupby The GROUPBY caluse.
 * @param  WP_Query $query   The current WP_Query object.
 * @return string            The GROUPBY clause.
 */ 
function custom_posts_groupby( $groupby, $query ) {
    
    global $wpdb;

    //* if is main query and a search...
    if ( is_main_query() && is_search() ) {
        $groupby = "{$wpdb->posts}.ID";
    }

    return $groupby;
    
}