It's not apparent what you are trying to do. Here's your code cleaned up with the syntax errors removed:

#!/usr/bin/perl

use strict;
use warnings;
use Data::Dumper;

my %hash=();
%hash=(
       ##keys between "" because of dots
       "M01.001" =>["M01.001"],
       "M01.001.111" =>["M01.001.111"],
       "M01.001.111.111" =>["M01.001.111.111"],
       "M01.002" =>["M01.002"],
       "M01.002.003" =>["M01.002.003"],
      );

print Dumper(%hash), "\n";

for my $k(sort keys %hash){
    my $temp = reverse($k);
    $temp =~ s/^\d{3}\.?//;
    my $t= reverse ($temp);
    if (exists $hash{$t}){
        $hash{$k}[1] += 1;
    }
}

print Dumper(%hash);

__END__
[download]

As for the $hash{$k}[1] += 1; "not working", it is working. It might not be doing what you wanted, but it's doing what somebody would expect, which is to create a second element in the array $hash{$k}, and then add 1 to it, to produce the result 1. If you meant to add 1 to the string "M01.001", what exactly do you think that means? You can't add the integer 1 to a string. It doesn't make sense.