you're pushing the same hash on the list, i think you want to make a copy yes?

my $data = [
    { cust_id => 1 },
    { cust_id => 3 },
];

my $order_data = {
    1 => { order_ids => '5,6' },
    3 => { order_ids => '7,8,9' },
};

my $output = [];
foreach my $hash (@$data) {
    my $cust_id = $hash->{cust_id};
    foreach my $id (split ',', $order_data->{$cust_id}->{order_ids}) {
        $hash->{order_id} = $id;
        push @$output, {%{$hash}};
    }
}
use Data::Dumper;
print Dumper $output;

__END__
$VAR1 = [
          {
            'cust_id' => 1,
            'order_id' => '5'
          },
          {
            'cust_id' => 1,
            'order_id' => '6'
          },
          {
            'cust_id' => 3,
            'order_id' => '7'
          },
          {
            'cust_id' => 3,
            'order_id' => '8'
          },
          {
            'cust_id' => 3,
            'order_id' => '9'
          }
        ];
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