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";
}
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