test.php

<?php

class A {

    /** @var \SplFixedArray */
    public $array;

    public function __construct(){
        $this->array = new \SplFixedArray(1);

        $b = new B();
        $b->value = uniqid();
        $this->array[0] = $b;
    }
}

class B {

    public $value;
}


$a = new A();

$a_clone = clone $a;
$a_clone->array[0]->value = uniqid();

var_dump([$a, $a_clone]);

//RESULT
array(2) {
  [0]=>
  object(A)#1 (1) {
    ["array"]=>
    object(SplFixedArray)#2 (1) {
      [0]=>
      object(B)#3 (1) {
        ["value"]=>
        string(13) "5b1bba5940d2f"
      }
    }
  }
  [1]=>
  object(A)#4 (1) {
    ["array"]=>
    object(SplFixedArray)#2 (1) {
      [0]=>
      object(B)#3 (1) {
        ["value"]=>
        string(13) "5b1bba5940d2f"
      }
    }
  }
}