What kind of website its ? any CMS or custom application ?

make sure directory setting exactly pointed. similar to this settings

<Directory "/home/public_html/DOMAIN.com/public">

#
# Possible values for the Options directive are "None", "All",
# or any combination of:
# Indexes Includes FollowSymLinks SymLinksifOwnerMatch ExecCGI MultiViews
#
# Note that "MultiViews" must be named *explicitly* --- "Options All"
# doesn't give it to you.
#
# The Options directive is both complicated and important. Please see
# http://httpd.apache.org/docs/2.2/mod/core.html#options
# for more information.
#
Options Indexes FollowSymLinks

#
# AllowOverride controls what directives may be placed in .htaccess files.
# It can be "All", "None", or any combination of the keywords:
# Options FileInfo AuthConfig Limit
#
AllowOverride All

#
# Controls who can get stuff from this server.
#
Order allow,deny
Allow from all

</Directory>