To exclude variations from sync - Product Catalog Sync for WooCommerce(https://www.webtoffee.com/product/product-catalog-sync-for-facebook/)

functions.php

add_filter( 'wt_facebook_sync_products', 'modify_wt_facebook_sync_products', 10, 1 );
function modify_wt_facebook_sync_products( $products ) {
	// modify the below example array $attr_taxonomies_term_slugs
	// Specify the array key as 'product attribute' and array elements as 'term slugs'
	$attr_taxonomies_term_slugs = array (	
		'pa_color' => array( 'blue', 'green', 'gray' ),
		'collar_type' => array( 'u-neck', 'v-neck', 'round' )
	);
    $exclude_products    = wt_get_variable_products_to_exclude($products, $attr_taxonomies_term_slugs);
    $sync_products       = array_diff( $products, $exclude_products );

    return $sync_products;
}
function wt_get_variable_products_to_exclude($products, $attr_list = array() ) {
	if( empty($attr_list) )
		return array();
	$meta_query_array = array('relation' => 'OR');
	foreach ( $attr_list as $attr_taxonomy => $attribute_term_slugs ) {
		$meta_query_array[] = array (
			'key' => 'attribute_' . $attr_taxonomy,
			'value' => $attribute_term_slugs,
			'compare' => 'IN'
		); 
	}

	$products = new WP_Query ( 
		array (
			'post_type'       => 'product_variation',
			'post_status'     => 'publish',
			'posts_per_page'  => -1,
			'post__in' 		  => $products,
			'meta_query'      => $meta_query_array,
			'fields' 		  => 'ids',	
		) 
	);
	if( $products->have_posts() ) {
		return $products->posts;
	}

	return array();	
}