As described in the documentation (Options with multiple values), you should use -prueba multiple times:

use strict;
use warnings;
use Data::Dumper;
use Getopt::Long;

my @array;

GetOptions ( 
                    "prueba2=s" => \@array,

 ) or die "not working: $!\n";

print Dumper(\@array);
exit;

__END__

foo.pl -p 1 -p 2 -p 3 
$VAR1 = [
          '1',
          '2',
          '3'
        ];
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