I've got the same issue on the newly installed vagrant box with Ubuntu 16.04.
Phalcon: 3.4.4
PHP: 7.3.8
Xdebug: 2.7.2 (also tested the current master branch with 3.0.0-dev)
Everything works without any issues in case Xdebug enabled in php.ini but XDEBUG_SESSION was not provided to the server.
Earlier I used Phalcon 3.3.1 with PHP 7.1.x and there were no such problems.

Remote debugging log with this script

<?php

$test = 5;
$config = new \Phalcon\Config(['test' => 45]); // <--- After that line debugger stop working
$yyy = $config->get('test');
var_dump($yyy);

I've tried to reproduce this, but I can't. @StudioMaX, can you share the Vagrant file?

You can test it here: https://github.com/StudioMaX/phalcon-xdebug
Just for your info:

• ssh keys are located in /ssh
• add 192.168.56.124 phalcon.test to your hosts
• test script located in /var/www/public/phalcon.php, can be accessed from http://phalcon.test/phalcon.php
• Phalcon v3.4.4 was compiled from source, you can recompile it via sudo compile-phalcon.sh
• sometimes Apache doesn't shartup on boot so you need to run sudo systemctl restart apache2

I haven't tried yet, but is it possible to reproduce on the CLI as well? /cc @StudioMaX

Well, when I run the Symfony Console in my app, which uses the Phalcon dependency manager, there are no issues. It also works if xdebug is enabled, but I do not use step-by-step debugging. But when I use step-by-step debugging, moved onto line $config = new \Phalcon\Config(['test' => 45]); and press F8, then Apache shows the HTTP 503 error page and writes "AH00491: caught SIGTERM, shutting down" into error.log. I can reproduce this error all the time.
A few days ago I upgraded PhpStorm to 2019.2.1, maybe this is related somehow.

@derick are you able to reproduce this case?

Well, it also crashes in CLI when using step-by-step debugging at the same breakpoint:
XDEBUG_CONFIG="idekey=PHPSTORM remote_autostart=1" PHP_IDE_CONFIG="serverName=phalcon_xdebug_cli" SITE_ENV="dev" php -dxdebug.remote_host=192.168.56.1 /var/www/public/phalcon.php

I tried to reproduce this again, but still no luck. Beyond Vagrant not working (it says something about not being able to find the provider?), it works locally without a hitch. However, this is with that latest RC candidate of Xdebug. Perhaps you can try that?

Yes, this still occurs on 2.8.0beta2.

Beyond Vagrant not working (it says something about not being able to find the provider?)
I use Windows as host and Ubuntu as guest in Virtualbox with Vagrant, maybe this is related somehow. But looks like the topic starter used native DLLs on Windows, so this is not related to Windows/Linux.

Could you provide something I can ssh into?

Hi there! I could successfully reproduce it with your Vagrant machine, and I know why I could reproduce it there, and not at home. At home I had compiled a beta of phalcon 4.0.0 (the master in git), and you were using 3.4.4. The 4 beta version handles data differently (or rather, correctly). I believe the bug is really in phalcon itself, but there is a workaround that I have that works around this. I'll have that committed later today (after it's gone through all the CI tests).

This is now fixed in GIT, for Xdebug 2.8.0beta3/RC1.