<?php
$a_controle = Array('A','B','C','D','E','F');
$array_final = Array(
    Array("A","B","C"),
    Array("A","B","D"),
    Array("A","C","E"),
    Array("D","E","F"),
    Array("A","B","P")
); 
 
$apareceu_com = Array();
 
foreach ($array_final as $sub_array_final){
    for ($i = 0; $i < count($sub_array_final); ++$i){
        for ($j = 0; $j < count($sub_array_final); ++$j){
            $elem1 = $sub_array_final[$i];
            $elem2 = $sub_array_final[$j];
 
            if ($i != $j){
                if (isset($apareceu_com[$elem1][$elem2])){
                    $apareceu_com[$elem1][$elem2]++;
                }
                else {
                    $apareceu_com[$elem1][$elem2] = 1;
                }
            }
        }
    }
}
 
print_r($apareceu_com);

PD9waHAKJGFfY29udHJvbGUgPSBBcnJheSgnQScsJ0InLCdDJywnRCcsJ0UnLCdGJyk7CiRhcnJheV9maW5hbCA9IEFycmF5KAogICAgQXJyYXkoIkEiLCJCIiwiQyIpLAogICAgQXJyYXkoIkEiLCJCIiwiRCIpLAogICAgQXJyYXkoIkEiLCJDIiwiRSIpLAogICAgQXJyYXkoIkQiLCJFIiwiRiIpLAogICAgQXJyYXkoIkEiLCJCIiwiUCIpCik7IAoKJGFwYXJlY2V1X2NvbSA9IEFycmF5KCk7Cgpmb3JlYWNoICgkYXJyYXlfZmluYWwgYXMgJHN1Yl9hcnJheV9maW5hbCl7CiAgICBmb3IgKCRpID0gMDsgJGkgPCBjb3VudCgkc3ViX2FycmF5X2ZpbmFsKTsgKyskaSl7CiAgICAgICAgZm9yICgkaiA9IDA7ICRqIDwgY291bnQoJHN1Yl9hcnJheV9maW5hbCk7ICsrJGopewogICAgICAgICAgICAkZWxlbTEgPSAkc3ViX2FycmF5X2ZpbmFsWyRpXTsKICAgICAgICAgICAgJGVsZW0yID0gJHN1Yl9hcnJheV9maW5hbFskal07CiAgICAgICAgICAgIAogICAgICAgICAgICBpZiAoJGkgIT0gJGopewogICAgICAgICAgICAgICAgaWYgKGlzc2V0KCRhcGFyZWNldV9jb21bJGVsZW0xXVskZWxlbTJdKSl7CiAgICAgICAgICAgICAgICAgICAgJGFwYXJlY2V1X2NvbVskZWxlbTFdWyRlbGVtMl0rKzsKICAgICAgICAgICAgICAgIH0KICAgICAgICAgICAgICAgIGVsc2UgewogICAgICAgICAgICAgICAgICAgICRhcGFyZWNldV9jb21bJGVsZW0xXVskZWxlbTJdID0gMTsKICAgICAgICAgICAgICAgIH0KICAgICAgICAgICAgfQogICAgICAgIH0KICAgIH0KfQoKcHJpbnRfcigkYXBhcmVjZXVfY29tKTs=