Reported for: WPML Multilingual CMS 3.3.8
The issue happens when you have taxonomy terms with the same name. Only one of the taxonomy terms is displayed and you are unable to translate it from the WPML->Taxonomy Translation or the WPML->WooCommerce Multilingual page.
Go to your taxonomy and edit the term with the same name. Inside the editing dialog box, there is a language subsection with a link that you can use to add a translation to that term.
This method is not using the WPML translation pages, but the ones provided by WordPress.