Try this, it might be what you are trying to achieve

#!perl
use strict;
use warnings;
use Data::Dumper;

my %input;
$input{12}[0] = "01-01-1989,ABC,12,12000,300000,Finanance,BC";
$input{12}[1] = "January,60000";

my @values;
my $table;

## add a table row counter
my $row=0;
## define the data array
my @data=();

foreach my $k (sort {$b <=> $a} keys %input) {
  foreach (@{$input{$k}}) {
    chomp();
  ##change this to use $row
  ##push( @{@data[$.]},( split /[,\n]/, $_));
    push( @{$data[$row]},( split /[,\n]/, $_));
  }
  # increment row for each key
  ++$row;
}
print "After\n";
print Dumper(\@data);

## add
my $body = "<table>";

for my $i ( 0 .. $#data ) {
  $body .= "<tr>";
## change this slightly
##for ( @{@data[$i]}){
  for ( @{$data[$i]}){
    $body .= "<td>$_</td>\r\n";
  }
  $body .= "</tr>";
  }
$body .= "</table>";
    
## result
print $body;
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