Some update. I was about to make a little script were I get the same backtrace on gdb every single time I run the php script.

Running MySQL  5.7.24, with a "test" table as followed, with a datetime(6) column. It seems to happen when using the "UPDATE" mysql function. No problem with a simple SELECT.

CREATE TABLE `test` (
  `id` int(11) NOT NULL,
  `date` datetime(6) NOT NULL,
  `poster_id` int(11) NOT NULL
) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_unicode_ci;


INSERT INTO `test` (`id`, `date`, `poster_id`) VALUES
(1, '2019-01-17 01:40:35.123456', 3);


PHP Script:

<?php

$dbh = "";
$dsn = 'mysql:host=localhost;dbname=testphp73';

// Set options
$options = [
    PDO::ATTR_PERSISTENT    => true,
    PDO::ATTR_ERRMODE       => PDO::ERRMODE_EXCEPTION
];

// Create a new PDO instanace
try {
    $dbh = new PDO($dsn, "root", "password", $options);
} // Catch any errors
catch (PDOException $e) {
    $this->error = $e->getMessage();
}


$stmt = $dbh->prepare("UPDATE test SET poster_id = 4 WHERE id = 1");

// no problem
// $stmt = $dbh->prepare("SELECT * FROM test WHERE id = 1");

$stmt->execute();


gdb backtrace with the UPDATE function:

(gdb) run test.php
Starting program: /usr/bin/php test.php
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
[Inferior 1 (process 6354) exited with code 01]
(gdb) b exit
Breakpoint 1 at 0x7ffff5d0a030: file exit.c, line 104.
(gdb) run test.php
Starting program: /usr/bin/php test.php
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".

Breakpoint 1, __GI_exit (status=1) at exit.c:104
104	exit.c: No such file or directory.
(gdb) bt
#0  __GI_exit (status=1) at exit.c:104
#1  0x00005555556319ed in ?? ()
#2  0x00005555557c2e1d in _efree ()
#3  0x00007ffff2d4fea7 in ?? () from /usr/lib/php/20180731/mysqlnd.so
#4  0x00007ffff2d4af4f in ?? () from /usr/lib/php/20180731/mysqlnd.so
#5  0x00007ffff2d4f641 in ?? () from /usr/lib/php/20180731/mysqlnd.so
#6  0x00007ffff2d4e0b9 in ?? () from /usr/lib/php/20180731/mysqlnd.so
#7  0x00007ffff2d4be04 in ?? () from /usr/lib/php/20180731/mysqlnd.so
#8  0x00007ffff2d4bf4e in ?? () from /usr/lib/php/20180731/mysqlnd.so
#9  0x00007fffed601ee4 in ?? () from /usr/lib/php/20180731/pdo_mysql.so
#10 0x00007ffff2b28d0c in ?? () from /usr/lib/php/20180731/pdo.so
#11 0x00007ffff2b2cbaa in ?? () from /usr/lib/php/20180731/pdo.so
#12 0x00005555557fc6ce in ?? ()
#13 0x00005555557f9371 in zend_hash_graceful_reverse_destroy ()
#14 0x00005555557e885e in ?? ()
#15 0x0000555555787662 in php_module_shutdown ()
#16 0x000055555564282a in ?? ()
#17 0x00007ffff5cf0830 in __libc_start_main (main=0x5555556423a0, argc=2, argv=0x7fffffffe5c8, init=<optimized out>,
    fini=<optimized out>, rtld_fini=<optimized out>, stack_end=0x7fffffffe5b8) at ../csu/libc-start.c:291
#18 0x0000555555642939 in _start ()
(gdb)

gdb backtrace when using SELECT function:

(gdb) run test.php
Starting program: /usr/bin/php test.php
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
[Inferior 1 (process 6387) exited normally]
(gdb) b exit
Breakpoint 1 at 0x7ffff5d0a030: file exit.c, line 104.
(gdb) run test.php
Starting program: /usr/bin/php test.php
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".

Breakpoint 1, __GI_exit (status=0) at exit.c:104
104	exit.c: No such file or directory.
(gdb) bt
#0  __GI_exit (status=0) at exit.c:104
#1  0x000055555564252d in ?? ()
#2  0x00007ffff5cf0830 in __libc_start_main (main=0x5555556423a0, argc=2, argv=0x7fffffffe5c8, init=<optimized out>,
    fini=<optimized out>, rtld_fini=<optimized out>, stack_end=0x7fffffffe5b8) at ../csu/libc-start.c:291
#3  0x0000555555642939 in _start ()
(gdb)

Given the use of persistent PDO connections and the efree() segfault during shutdown, this is very likely a duplicate of bug #77289, which will be fixed in PHP 7.3.2.