I was somewhat led down the garden path recently with an error on a Cpanel system recently that turned out to be a permissions issue.
It turns out that incorrect permissions can cause a 500 (Internal Server Error), rather than the 403 (Forbidden) that I had expected. For example, if a file’s owner and/or group is root, a 500 Error occurs.
Interstingly CPanel’s Apache config also has some security setting that will also return a 500 Error on any php script that is writable by the group. Nothing a chmod 644 *.php can’t fix though.