Reported for: WooCommerce Multilingual 3.6.4
Resolved in: WooCommerce Multilingual 3.6.5
The product variations don’t sync correctly when the term used for generating the variations is in the situation that the term_id value in the database is different than the value of term_taxonomy_id.
1. Download WooCommerce Multilingual 3.6.5-beta1 from the WPML.org downloads page.
2. Run the variations synchronization again or update the original product.