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This error comes from mod_evasive
apache module.
I had installed Apache mod_evasive for DoS protection, and I did not know that just by installing this module it affects Apache and on Debian default (non-existing) configuration for this module is quite aggressive for modern service-based web applications.
I created /etc/apache2/mods-available/mod-evasive.conf
as a default config for this module with higher limits and problem solved.
Source:stackexchange.com