Problem:
Product attribute terms with the same slug (using the method described here https://wpml.org/errata/translated-term-slug-identical-to-the-original-term-slug/) are assigned to the wrong language product with the wrong term count. This happens only after using the sync feature in WooCommerce → WooCommerce Multilingual → Attributes → Sync variations.
Solution:
Update the WooCommerce Multilingual to the latest version but if you're using the version prior to 4.12.0, go to /wp-content/plugins/woocommerce-multilingual/inc/translation-editor folder, and edit the class-wcml-synchronize-product-data.php file. Just look for this line of code:
if ( is_taxonomy_hierarchical( $taxonomy ) ) {
and replace it with
if ( is_taxonomy_hierarchical( $taxonomy ) || true ) {
Once you did this, just simply synchronize again the terms and the count will work fine.