WordPress Pages Redirecting to Root with WordPress Multisite (Sub-Directory)

Check your rewrites to make sure it follow this

 if (!-e $request_filename) {
    rewrite ^/[_0-9a-zA-Z-]+(/wp-.*) $1 last;
    rewrite ^/[_0-9a-zA-Z-]+.*(/wp-admin/.*\.php)$ $1 last;
    rewrite ^/[_0-9a-zA-Z-]+(/.*\.php)$ $1 last;
}

not this

  if (!-e $request_filename) {
        rewrite /wp-admin$ $scheme://$host$request_uri/ permanent;
        rewrite ^(/[^/]+)?(/wp-.*) $2 last;
        rewrite ^(/[^/]+)?(/.*\.php) $2 last;
    }