Your code would work as expected if $VAR2 were a reference to a single hash rather than a reference to an array with one element (a hash ref).

#!/usr/bin/perl -w

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


my $VAR1 = {
          'Total' => {
                       'month1' => 0,
                       'month2' => 0,
                       'month3' => 0,
                       'month4' => 0,
                       'month5' => 0,
                       'month6' => 0,
                       'month7' => 0,
                       'month8' => 0,
                       'month9' => 0,
                       'month10' => 0,
                       'month11' => 0,
                       'month13' => 0,
                       'month14' => 0,
                       'month15' => 0,
                       'month16' => 0
                     },
          'Tom' => {
                                'month1' => 17,
                                'month2' => 1,
                                'month3' => 15,
                                'month4' => 0,
                                'month5' => 3,
                                'month6' => 30,
                                'month7' => 33,
                                'month8' => 0,
                                'month9' => 0,
                                'month10' => 0,
                                'month11' => 0,
                                'month12' => 0,
                                'month13' => 0,
                                'month14' => 0,
                                'month15' => 0
                              }

        };


my $VAR2 =
          {
            'Total' => {
                         'week1' => 0,
                         'week2' => 0,
                         'week3' => 0
                       },
            'Harry' => {
                          'week1' => 0,
                          'week2' => 5,
                          'week3' => 5
                       }

          };


    my %joined_FS;
    $joined_FS{$_} ||= {( %{$VAR1->{$_}||{}}, %{$VAR2->{$_}||{}} )} fo
+r keys(%$VAR1), keys(%$VAR2);
    #This example was given by PerlMonks
    print Dumper(\%joined_FS);



OUTPUT:
$VAR1 = {
          'Tom' => {
                     'month10' => 0,
                     'month11' => 0,
                     'month15' => 0,
                     'month6' => 30,
                     'month7' => 33,
                     'month5' => 3,
                     'month13' => 0,
                     'month12' => 0,
                     'month4' => 0,
                     'month9' => 0,
                     'month3' => 15,
                     'month1' => 17,
                     'month2' => 1,
                     'month8' => 0,
                     'month14' => 0
                   },
          'Total' => {
                       'week3' => 0,
                       'month6' => 0,
                       'week1' => 0,
                       'month10' => 0,
                       'month8' => 0,
                       'month2' => 0,
                       'month4' => 0,
                       'month5' => 0,
                       'month7' => 0,
                       'month15' => 0,
                       'month11' => 0,
                       'month14' => 0,
                       'month16' => 0,
                       'month1' => 0,
                       'month3' => 0,
                       'month9' => 0,
                       'month13' => 0,
                       'week2' => 0
                     },
          'Harry' => {
                       'week3' => 5,
                       'week1' => 0,
                       'week2' => 5
                     }
        };
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