<?php
$mysql = array( '01', '03', '04', '06', '11' );

$max = max(12, max($mysql));

$final = array();

for ($i = 1; $i <= $max; $i++) {

    $current = str_pad($i, 2, '0', STR_PAD_LEFT);
    
    if (in_array($current, $mysql)) {
        $final[] = $current;
    } else {
        $final[] = '00';
    }
}

print_r($final);