In Apache 2.4 access control has changed, so the .htaccess files should be changed for compatibility.
deny from all
should be changed to
<IfVersion <= 2.2>
Deny from all
<IfVersion >= 2.3>
Require all denied
2.3 is the development version of 2.4.
Because this is dependent on mod_version, a commented central .htaccess file in document root directory should be used, so users can easily change it if mod_version is not available.
See "Access control" on http://httpd.apache.org/docs/2.4/en/upgrading.html