During analysis, I found that this only happens when the destructors are called when the object goes out of the global scope only.

For example, this version does not show the same behaviour:

<?php
class Testing
{
    function __destruct() {
        echo "Destruct";
    }
}

function a() {
    $t = array();
    for ($i=0; $i<5; $i++) {
        $t[] = new Testing();
    }
}

a();

https://github.com/xdebug/xdebug/pull/1004