If I recall correctly, WooCommerce adds those menu items "for internal use". Normally it deletes them just before the final admin menu is displayed, but with AME active that doesn't work as expected because it sees the menus before they're deleted. Unfortunately, this is not really fixable.
What you could do is hide the extra menu items. Try enabling the "show/hide" button in AME settings (click the "Settings" link next to the "Menu Editor" page title).
In case you're interested, here's basically what happens when you load an admin page:
- WordPress creates the default admin menu.
- WooCommerce adds a bunch of menu items.
- Other plugins add their own items.
- Admin Menu Editor makes a copy of the entire admin menu and applies your custom settings (if any) to the copy.
- WooCommerce deletes the extra menu items. This does not affect the copy that AME has.
- Admin Menu Editor replaces the default admin menu with the customized copy.
- WordPress displays the admin menu.