Isso se deve à try_files
loucura e outras abordagens questionáveis. Remova todos os seus exercícios e torne-o canônico:
location / {
index index.html;
if (!-e $request_filename) {
rewrite ^/(.*)$ /index.php;
}
}
location ~ \.php$ {
include /etc/nginx/fastcgi_params;
fastcgi_param SCRIPT_FILENAME $document_root$fastcgi_script_name;
fastcgi_param QUERY_STRING $query_string;
fastcgi_pass 127.0.0.1:9000;
fastcgi_intercept_errors on;
fastcgi_cache default;
break;
}