update
The script is index.cgi, copied by the install.sh script. the script is okay, i can run it in a virtual debian with similar settings ( apache, perl version )
Checked apache logs and found this line only nothing else.

Tue Sep 29 08:55:54 2015] [info] [client 10.10.10.2] Connection closed
+ to child 3 with standard shutdown (server my.test.gestio.hu:443)
[Tue Sep 29 08:55:56 2015] [info] [client 10.10.10.2] Connection to ch
+ild 4 established (server my.test.gestio.hu:443)
[Tue Sep 29 08:55:56 2015] [info] Seeding PRNG with 656 bytes of entro
+py 
[Tue Sep 29 08:55:56 2015] [info] Initial (No.1) HTTPS request receive
+d for child 4 (server my.test.gestio.hu:443) 
[Tue Sep 29 08:55:56 2015] [error] [client 10.10.10.2] Premature end o
+f script headers: index.cgi 
[Tue Sep 29 08:55:56 2015] [info] [client 10.10.10.2] Connection close
+d to child 4 with standard shutdown (server my.test.gestio.hu:443) 
[Tue Sep 29 09:43:56 2015] [info] [client 10.10.10.2] Connection to ch
+ild 5 established (server my.test.gestio.hu:443) 
[Tue Sep 29 09:43:56 2015] [info] Seeding PRNG with 656 bytes of entro
+py 
[Tue Sep 29 09:43:56 2015] [info] Initial (No.1) HTTPS request receive
+d for child 5 (server my.test.gestio.hu:443) 
[Tue Sep 29 09:43:56 2015] [info] [client 10.10.10.2] Connection close
+d to child 5 with standard shutdown (server my.test.gestio.hu:443) 
[Tue Sep 29 09:44:00 2015] [info] [client 10.10.10.2] Connection to ch
+ild 9 established (server my.test.gestio.hu:443) 
[Tue Sep 29 09:44:00 2015] [info] Seeding PRNG with 656 bytes of entro
+py 
[Tue Sep 29 09:44:05 2015] [info] Initial (No.1) HTTPS request receive
+d for child 9 (server my.test.gestio.hu:443) 
[Tue Sep 29 09:44:05 2015] [error] [client 10.10.10.2] Premature end o
+f script headers: index.cgi 
[Tue Sep 29 09:44:05 2015] [info] [client 10.10.10.2] Connection close
+d to child 9 with standard shutdown (server my.test.gestio.hu:443)
[download]

I try to run another .cgi perl script, but get the same error always.
i do not use fasrcgi or suexec, i have read they could made similar errors.
I have a goog running system as well with this script, so i just need to figure out the difference what cause this error.