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}

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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()));
}