Попробуйте заменить $ numbers на содержимое файла csv.
$numbers = array('+1134124', '+11412421', '+41125125','+41125124','+41125144','+41155124','+44125124','+44155124');
$final = array();
$received = array();
foreach($numbers as $snKey => $snValue )
{
$snCode = substr($snValue,0,3);
if(in_array($snCode,$received))
continue;
else
{
$received[] = $snCode;
$final[] = $snValue;
}
}
print_r($final);