<?php
 
$texto = 
'ID|NOME|TELEFONE0|ENDERECO|REFERENCIA-
ID|NOME|TELEFONE1|ENDERECO|REFERENCIA-
ID|NOME|TELEFONE2|ENDERECO|REFERENCIA-
ID|NOME|TELEFONE0|ENDERECO|REFERENCIA';
 
$item = explode("-", $texto);
 
$items = array_map(function($line)
{
    return explode("|", $line);
}, $item);
 
$repeat = [];
 
foreach($items as $it)
{		
    $repeat[$it[2]] = 
	isset($repeat[$it[2]])	
	? (++$repeat[$it[2]])
	: 1;	
}
 
$select = array_filter($repeat, function($item){
    return $item > 1;
});
 
echo '<pre>';
print_r($repeat);
print_r($select);
echo '<pre>';

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