1. It's difficult to explain... You could comment out my code change and run my written test with debugger. Pay attention at ArrayHydrator:135 when the phone number mapping is being set. After setting 'Article 1' phone number elements, you will get $this->_identifierMap values (I'm only adding u.p relationship here):

[
    'u.p' => [
        '|1' => [
            '|1234567890' => '0',
            '|9876543210' => '1',
        ],
    ],
]

So far, everything works as expected, but then comes 'Article 2' phone numbers in different order than before. If $this->_identifierMap['u.p']['|1'] values are not reset, algorithm gets array index of 9876543210 number from mapping. Index is 1, but on line 135 |9876543210 value in $this->_identifierMap will be overridden to 0 and mapping will look like this:

[
    'u.p' => [
        '|1' => [
            '|1234567890' => '0',
            '|9876543210' => '0',
        ],
    ],
]

Two array elements with different keys, but same values. That will cause unexpected behavior in updateResultPointer method called on line 154. Then, on line 268 if statement will be valid with $index = 1, but $coll will only have one element as the only the first phone number was set till this point (second phone number will be set on next iteration):

$coll = [
    0 => [
        'phonenumber' => '9876543210',
    ],
];

Because of that, on line 269 $coll[1] is treated as null and this is the line where those null values are being set.
So, resetting $this->_identifierMap of base element children each time the new to-many relation is added to base element solves this problem, because new elements are not getting previous element indexes. It may not be the best solution, but it works. I am not deeply familiar with Doctrine internals.
Also, it may not be any easier to understand the bug after my explanation, but I tried my best.

2. I have run the benchmark, didn't notice performance difference between current and modified version.

Also, while trying to explain this bug right now, I noticed another problem. If you changed the order of article rows in my test case (order by ids: 1, 2, 1, 2), results would be interesting, too.

Thanks for your explanation! I can't say it helps me because I too am not very familiar with that part of the code, but I will try to get the right people to review this.

Does ObjectHydrator have similar code to handle this already? I find it strange this never came up before.

I am confused why its nested, since you dont fetch the object but properties. Can you turn this into a real DQL query as per your comment? I am wondering if the problem is just a wong ResultSetMapping

Yeah, query didn't correspond to what I was trying to accomplish. I updated it, I want nested results.

Is anybody looking at this issue? I don't want it to be forgotten.

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