You need to change the structure to $pivot{$app}{$device}{$browser}

#!/usr/bin/perl
use strict;
use warnings;
use Excel::Writer::XLSX;

# set up with test data
my @responseid; my @responsdisp; my @responsalter;
my @responseclientdevice; my @responseclientbrowser;
my @responseapps5; my @estdate;
test_data();

my $strExcelFilename= 'chart.xlsx';
my $book = Excel::Writer::XLSX->new($strExcelFilename);
my $format = $book->add_format(); 

my $worksheet1 = $book->add_worksheet('Data');
my @header = ('User Id','User Display Name','User Email Id','Device',
              'Browser','Application Name','Timestamp'); 
$worksheet1->write(0,0, \@header, $format);          
            
my $row1 = 1;
my %pivot=(); # pivot table count
my %categ=();
my %app  =();

for my $k (0..$#responseid)  {
  my @f = (
   $responseid[$k],  #0
   $responsdisp[$k], #1
   $responsalter[$k],#2
   $responseclientdevice[$k], #3
   $responseclientbrowser[$k],#4
   $responseapps5[$k],        #5
   $estdate[$k],              #6
  );
  $worksheet1->write($row1,0, \@f);
   
  my $device  = $f[3];
  my $browser = $f[4];
  my $app     = $f[5];
        
  ++$pivot{$app}{$device}{$browser};
  ++$categ{'device'}{$device};
  ++$categ{'browser'}{$browser}; 
  ++$app{$app};
    
  $row1++;
  #print Dumper $app;   
}

# create summary pivot table
my $worksheet2 = $book->add_worksheet('Summary');
my @device  = sort keys %{$categ{'device'}};
my @browser = sort keys %{$categ{'browser'}};
my @applist = sort keys %app;

$row1 = 0;
for my $device (@device){
  $worksheet2->write($row1++,0,[$device,@applist]);
  for my $browser (@browser){
    my $col = 0;
    $worksheet2->write($row1,0,$browser);
    for my $app (@applist){
      $worksheet2->write($row1,++$col,$pivot{$app}{$device}{$browser})
+;
    }
    ++$row1;
  }
  ++$row1;
}

sub test_data {
  while (<DATA>)  {
    chomp;
    next unless /\S/;
    my ($userid,$device,$browser,$app) = split ';',$_;
    push @responseid,$userid;
    push @responseclientdevice,$device;
    push @responseclientbrowser,$browser;
    push @responseapps5,$app; 
  }
}
__DATA__
user1;Mobile;Chrome;AppA
user2;Mobile;IE11;AppB
user3;Computer;IE11;AppC
user4;Mobile;Chrome;AppD
user5;Computer;Firefox;AppA
user6;Tablet;IE11;AppC
user7;Tablet;Safari;AppE
user8;Computer;Safari;AppE
user9;Computer;Safari;AppE
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