• please use a consistent way of intendation; it makes the code more readable; I think perlstyle has something about that.
• the mix of english and italian variable names doesn't help to understand the code
• the italian comments don't help those who don't speak Italian
• your regex cannot match, as you use (\.\+) in it, but where in your data source is the string .*?
• Is it correct, that in your data source, some lines use '*', other '.*' to separate the items per line?
• you use \s{0,2} in your regex; making it something like "string(0-2 whitespaces)string"; but I saw s/th like "string(3 whitespaces)string" in your data source; maybe you should consider using \s*

update

1. question changed
2. +: whitespace regex
3. fixed typo

perltidy helps with the formatting

#!/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;
[download]

OK, a typo in the previous reply.



$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){
[download]


should read



$conto++ if $text =~/(($key\/$key\/S)\s{0,2}(\.\*)\s{0,2}(con\/con\/E)
+\s{0,2}(\.\*)\s{0,2}($value\/$value\/S))/is){
[download]

Thanks for the comment.
But if I try using your code, I get the same result as mine. Every couple has the same number of occurrences, and that just isn't possible. I'm sorry if I cannot make it more clear, is just I don't know how to explain that.

I think your problem is, that you only have one counter variable, which is increased for each individual matching.

Consider something like this:

#my $conto = 0;                 #### REMOVED; not needed
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){
      ### increase for each key/value pair individually
      $arrayris{ join '-', $key, $value }++;
    }
  }
}
while ( my ($k,$v) = each %arrayris ) {
  print CONTEGGIO "($k) => $v\n";
}
[download]

#!/usr/bin/perl
use strict;
use warnings;
open my $listaParole,"File_Input/Coppie_Parole.txt" or die;
 
my %hash;
while (my $line=<$listaParole>) {
  chomp $line;
  my ($word1, $word2) = split /:/, $line;
  $hash{$word1} = $word2;
}
close $listaParole;

open my $testo, "<Wiki_Pulito/Prova/Pattern2.txt" or die;  
open my $conteggio, ">Wiki_Pulito/Prova/Conteggio1.txt" or die;

my $count=0;
my %arrayris;

    while (my $text=<$testo>){
       for my $key (keys %hash){
     my $value = $hash{$key};
     if ($text =~/($key\/$key\/S)\s{0,4}(\.\*)\s{0,4}(con\/con\/E)\s{0
+,4}(\.\*)\s{0,4}($value\/$value\/S)\b/g){
                        $count++;
                }  

     my $arrkey=$key."-".$value;
     $arrayris{$arrkey}=$count;
           }
     }

while ( my ($k,$v) = each %arrayris ) {
    print $conteggio "($k) => $v\n";
  
}
close $testo;
close $conteggio;
[download]

([aA]mplificator[ei]-[Tt]ransistor) => 27
([cC]ervello-[Tt]alamo) => 27
([Ee]ucariot[ia]-[Mm]embran[ae]) => 27
([Cc]erio-[Ii]sotop[oi]) => 27
([Cc]ellul[ae]-[Nn]ucle[oi]) => 27
([Tt]ronco-[Tt]orace) => 27
([Bb]raccio-[Aa]vambraccio) => 27
[download]

Did you see and consider my reply (though its based upon u67129's code)?

No. I just saw and tried it. It works now, perfectly fine. Thank you so much! You have no idea how much I appreciate it!