try below config, also check bootstrap init if it has 'index_file' => FALSE.
server {
listen 80;
server_name *.domain.com;
client_max_body_size 20M;
access_log /home/user/public_html/site/log/access.log;
error_log /home/user/public_html/site/log/error.log;
root /home/user/public_html/site/public/;
index index.php;
location / {
# don’t check $uri/, send to php for nice error message
try_files $uri /index.php?$query_string;
}
location = /index.php {
include fastcgi.conf;
fastcgi_pass 127.0.0.1:9000;
fastcgi_index index.php;
}
}