It does not depend on multisite or not. The problem is coming from the taxonomy management in WordPress.
Nav menus, categories, post tags and languages are taxonomies. When you use the same name accross several taxonomies, by default, only one term is created.
Polylang normally includes a workaround against this. It works well for categories and post tags. And I discovered today that this protection does not work for nav menus because of a bug I reported. This is easy to correct but of course any modification in WordPress needs deep testing, to be sure that it does not break something else.
Waiting for this, one should not create a menu with the same name as a language. I will add a notice with the next version and go on working on this topic to see if I can improve the situation on Polylang side.