<?php

$arr = [
    ['pivot' => ['milestone_id' => 1]],
    ['pivot' => ['milestone_id' => 2]],
    ['pivot' => ['milestone_id' => 3]],
    ['pivot' => ['milestone_id' => 4]],
];

$output = array_map(function($data){
    return $data['pivot']['milestone_id'];
}, $arr);

print_r($output);