Just had a wierd issue where my javascript was not loading. It boiled down to a alias in lighttpd that was causing the issue. The culprit is Debian package javascript-common which installs an alias to alias /javascript to a local directory.
The file is called 90-javascript-alias.conf which is in /etc/lighttpd/conf-enabled folder. Removing the 90-javascript-alias.conf symlink and restarting the server solved it.