These kind of error can be seen in /var/log/messages in a cpanel cloudlinux based server which will be filling the /var/log/messages quickly.
This can be caused due to below reasons :
1. You are running php as CGI and if that is the case, you can ignore this error and you can get this fixed by simply upgrading to the latest LVE kernel.
2. This happens due to conflict between mod_hostinglimits and mod_fcgid . In such cases, try disabling the mod_hostinglimits and see if that resolves the issue. If it fixes the issue, then
Edit “/usr/local/apache/conf/modhostinglimits.conf” and remove the handlers which are handled by mod_fcgid.
(I simply commented the AllowedHandlers line completely which stopped those errors)
3. Another reason may be crond/httpd running inside LVE. This usually happens if you su/sudo to root using non-wheel user.
More details can be gained from the below Cloudlinux Forums / may need to contact their support