I even tried reinstalling Ubuntu and everything (leaving default config), but it produces the same error.

There can be plenty of reasons why, especially since Phalcon is involved.

I would start with disabling xdebug and opcache (at least temporarily) to figure out if these are the culprits.

Im starting to think that there is some problem with my phalcon app.

Ill try with a fresh installation to see what happens and post the results here.

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We have plenty of visitors during the day and site works fine.

Not only that but errors in log repeat in same pattern, sometimes every 10 seconds, sometimes 20 sec.

PHP log has this issues during that time (plenty of those, this is just one example).

It was JotCache plugin in joomla, starting every day at the same time and doing nasty stuff in mysql.

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Squid 54 Connection Reset By Peer Nginx Php