Ignore queries having 3 posts per page

<?php

// Add the following to your (child) theme's functions.php

add_filter( 'facetwp_is_main_query', function( $is_main_query, $query ) {
    if ( 3 == $query->get( 'posts_per_page' ) ) {
        $is_main_query = false;
    }
    return $is_main_query;
}, 10, 2 );