You have not specified exactly what is required for your 'missing keys' test case. There is a very subtle difference between $data_hash->{c}->[2] = undef and $data)hash->{c}->[2] does not exist. I assumed that it should be undef. This requires setting the length of the arrays. The following test passes. Try commenting out the statement with '# Set length'. Observe how the test fails.

use strict;
use warnings;
use Test::More tests=>1;

my $data = [
  {a => 1, b => 2, c=>11},
  {a => 3,         c=>12},
  {a => 5, b => 6},
];
my $required = {
    a => [1, 3,     5    ],
    b => [2, undef, 6    ],
    c =>[11, 12,    undef],
};

my $data_hash;
foreach my $i (0..$#$data) {
    while ((my $key, my $value)= each %{$data->[$i]}) {
        $#{$data_hash->{$key}} = $#$data;   # Set length
        $data_hash->{$key}->[$i] = $value;
    }
}
is_deeply($data_hash, $required, 'missing keys');
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Of course, if you require c => [11, 12] then the "set length" statement must be omitted.