Проверьте подключение компонента сравнения товаров. Там должен быть прописан IBLOCK_ID, такой же что и у вашего каталога.
<?php $APPLICATION->IncludeComponent(
"bitrix:catalog.compare.list",
"header",
Array(
"ACTION_VARIABLE" => "action",
"AJAX_MODE" => "Y",
"AJAX_OPTION_ADDITIONAL" => "",
"AJAX_OPTION_HISTORY" => "N",
"AJAX_OPTION_JUMP" => "N",
"AJAX_OPTION_STYLE" => "Y",
"COMPARE_URL" => "/catalog/compare/",
"DETAIL_URL" => "/catalog/#SECTION_CODE_PATH#/#ELEMENT_CODE#/",
"IBLOCK_ID" =>"Ваш ID инфоблока",
"IBLOCK_TYPE" => "Ваш тип инфоблока",
"NAME" => "CATALOG_COMPARE_LIST",
"POSITION" => "top right",
"POSITION_FIXED" => "N",
"PRODUCT_ID_VARIABLE" => "id"
)
);?>