<?php

$array = array (
    0 => array (
        0 => 'valor1', 
        2 => 'valor2', 
    ),
    1 => array (
        0 => 'valor3',
        1 => 'valor4',
        3 => 'valor5'
    )
);


for($i=0; $i<count($array); $i++){
	$array[$i] = array_values($array[$i]);	
}

print_r($array);