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This thread is resolved. Here is a description of the problem and solution.
Problem: Sitemap generated with Jetpack shows duplicate entries.
Solution: Jetpack's Sitemap module is using custom SQL queries directly to the database so WPML's filters don't have any effect. Hence it detects the are two copies of each post and page but it does not detect the language of those entries.
This will be escalated to our compatibility team for further investigation but it will take time. However, there are other plugins that have been tested: https://wpml.org/documentation/plugins-compatibility/?wpv_post_search=seo