The keys for the array passed to register_nav_menus() should correspond with the 'theme_location' arguments in your calls to wp_nav_menu(). Since they do not, WordPress is unable to locate the appropriate menu and displays a default consisting of all top-level pages instead.
Either change your 'theme_location' arguments to 'menu-1' and 'menu-2' or change the array keys in your register_nav_menus() call to 'primary' and 'secondary'.
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