Plugins with nested folders not uploading properly

We seem to have an ongoing issue with the WordPress plugin update system. I’ve tested it with a couple of plugins but Visual Composer is the one I notice it most with. It occurs in Visual Composer and other plugins that have a folder structure like this /plugins/visualcomposer/visualcomposer

When running an update for whatever reason the second-level visualcomposer folder gets deleted which results in this error.

Uncaught Error: Failed opening required '/www/wp-content/plugins/visualcomposer/visualcomposer/Env.php' (include_path='.:/usr/share/php') in /www/wp-content/plugins/visualcomposer/plugin-wordpress.php:102

It only appears to happen if you upload the plugin through the plugin page in the admin. If you manually upload the folder it is fine. I’d assume it’s something to do with how the zip gets unpacked and put into the plugin folder.

Has anyone dealt with this and does anyone have the time to debug it and work out what code is causing the problem to submit a bug to Trac??