Hi,
It would help if you presented less data and your examples reflected the data you are using.

Some initial thoughts:
1) The while loop around the Regex will be infinite if a match is found. I think that should read
$conto++ if $value =~/(($key\/$key\/S)\s{0,2}(\.\*)\s{0,2}(con\/con\/E)\s{0,2}(\.\*)\s{0,2}($value\/$value\/S))/is){
2) The while, open & close statements can be improved see below 3) You are inconsistent with your die and close statements, perhaps because you haven't got round to tidying them up yet
4) The con\/con\/E part of the Regex probably needs to be in a variable so you can loop through the other possibilities e.g. "dalla/da/E"
5) As your Regex is ignoring case the e.g. Nnoption is redundant.

The following code seems to work and incorporates some of the above points. I've also simplified the Regex as the example data works with this Regex.

#!/usr/bin/perl
use strict;
use warnings;
open( INPUT, "<Wiki_Pulito/Prova/Pattern2.txt") or die "Can't open Pat
+tern2.txt";
open( LISTAPAROLE,"<File_Input/Coppie_Parole.txt") or die "Can't open 
+Coppie_Parole.txt";

my %hash;
while (<INPUT>) {
        chomp;
        my ($word1, $word2) = split /:/, $_;
        $hash{$word1} = $word2;
}
close INPUT;

# Carico la parte di file di testo che va analizzata
open( CONTEGGIO, ">Wiki_Pulito/Prova/Conteggio.txt") or die "Can't ope
+n Conteggio.txt";
# Apro il file di output
my $conto=0;
my %arrayris;
while (my $text = <LISTAPAROLE>){
        for my $key (keys %hash){
                my $value = $hash{$key};
                if ($text =~/$key\/$key\/.*con\/con\/E.*$value\/$value
+\/S/is){
                        $conto++;
                }
                my $arrkey=$key."-".$value;
                $arrayris{$arrkey}=$conto;
        }
}
while ( my ($k,$v) = each %arrayris ) {
    print CONTEGGIO "($k) => $v\n";

}
close LISTAPAROLE;
close CONTEGGIO;
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