Why array_unique does not detect duplicate objects?

For your issue at hand, I am really suspecting this is coming from the way array_unique is removing elements out of the array, when using the SORT_REGULAR flag, by:

1. sorting it
2. removing adjacent items if they are equal

And because you do have a Proxy object in the middle of your User collection, this might cause you the issue you are currently facing.

This seems to be backed up by the warning of the sort page of PHP documentation, as pointed out be Marvin's comment.

Warning Be careful when sorting arrays with mixed types values because sort() can produce unexpected results, if sort_flags is SORT_REGULAR.

^{Source: https://www.php.net/manual/en/function.sort.php#refsect1-function.sort-notes}

Now for a possible solution, this might get you something more Symfony flavoured.

It uses the ArrayCollection filter and contains methods in order to filter the second collection and only add the elements not present already in the first collection.
And to be fully complete, this solution is also making use of the use language construct in order to pass the second ArrayCollection to the closure function needed by filter.

This will result in a new ArrayCollection containing no duplicated user.

public static function merge(Collection $a, Collection $b, bool $unique = false): Collection {
  if($unique){
    return new ArrayCollection(
      array_merge(
        $a->toArray(),
        $b->filter(function($item) use ($a){
          return !$a->contains($item);
        })->toArray()
      )
    );
  }

  return new ArrayCollection(array_merge($a->toArray(), $b->toArray()));
}

I know that you said that you don't want converting to string, but i see that you are yet no have way out, so i propose to you use the function serialize to each object in your array, i don't found a method to compare objects that isn't converting in array or string (you cant try convert in binary or hex if you don't unfamiliar with string or array, but i don't know if you can converting to binary or hex without to convert in string).

But, if you use serialize, you can serialize the object in a read data own of php, to you compare with anothers serialized objects, this method (serialize) is safe, because you can do aunserialize, and geting the original object again.

So you can serialize all elements from array and after this, you can use array_unique, like that:

<?php

header("Content-Type: application/json");

class MyClass
{
    public $var1;
    public $var2;
    function __construct($var1, $var2)
    {
        $this->var1 = $var1;
        $this->var2 = $var2;
    }

}

$arr = [
    "a",
    "a",
    [1,2,3],
    "b",
    [1,2,3],
    new MyClass(1,1),
    new MyClass(1,new MyClass(1,1)),
    new MyClass(1,new MyClass(1,1)),
];

$arrSerilized = array_map("serialize", $arr);

var_dump(
    array_map(
        "unserialize",
        array_unique(
            $arrSerilized,
            SORT_STRING
        )
    )
);

/* output:
array(5) {
    [0]=>
    string(1) "a"
    [2]=>
    array(3) {
        [0]=>
        int(1)
        [1]=>
        int(2)
        [2]=>
        int(3)
    }
    [3]=>
    string(1) "b"
    [5]=>
    object(MyClass)#6 (2) {
        ["var1"]=>
        int(1)
        ["var2"]=>
        int(1)
    }
    [6]=>
    object(MyClass)#7 (2) {
        ["var1"]=>
        int(1)
        ["var2"]=>
        object(MyClass)#8 (2) {
            ["var1"]=>
            int(1)
            ["var2"]=>
            int(1)
        }
    }
}
*/

Hope this help you man, have a good day!

P.S.: With serialize you can preserve same value in different variable type, like 1 and "1" are serialized in different read data of php

Without knowing about your entity class its hard to guess why this is happening. But I guess your main issue here is __toString() method . If you have not defined it, you should add one such that it returns a unique/distinct string for each entity object. If its already defined make sure it returns distinct string.

class User{ 
   private $name;

   function __construct($name){ 
      $this->name=$name;
   }

   function __toString(){ 
     return $this->name; 
   }
}

$user = [];
$users[] = new User("User1");
$users[] = new User("User2");
$users[] = new User("User3");

$user1= $users[0];
$users[]=$user1; //duplicate

echo(count(array_unique($users))); // output should be 3

Given the limited information about entity class I can guess this far.

Edit:

After reading your edits I guess you are locking yourself into this. Since array_unique will try to convert an entity object to either string or number depending on the sort_flag you pass. More on array_unique. So either you need to implement __toString() or add some public properties which define the uniqueness of your object to entity e.g

class User{ 
       public $id;
       private $name;

       function __construct($id,$name){
          $this->id=$id;
          $this->name=$name;
       }
}

$user = [];
$users[] = new User(1,"User1");
$users[] = new User(2,"User2");
$users[] = new User(3,"User3");

$user1= $users[0];
$users[]=$user1; //duplicate
echo(count(array_unique($users, SORT_REGULAR))); // output should be 3

Please note the public property $id and SORT_REGULAR flag.