Locale URL segment being duplicated, eg https://website.test/en/en/
Your issue is that the @web alias resolves to this:


  The URL to the folder that contains the index.php file that was loaded for the request


Now that you’re serving your English site from web/en/index.php, @web will already resolve to http://website.test/en.

The alias @web/en you are using for your site’s base URL does therefore resolve to http://website.test/en/en

So you can fix it be using @web for your base URLs, or what I would rather recommend is to serve all your sites from a single web/index.php file (which is possible now in Craft 3). With this change @web will always refer to http://website.test and you need to use @web/en again in your site settings.