I am having a problem with returning multiple hashes from a subroutine.

I'm not even a little surprised. In fact you can't even return a single hash from a sub. Only a list. If the list consists of key-value pairs, then it can be conveniently assigned to a hash. Otherwise, it can contain quite about anything, including hashrefs:

#!/usr/bin/perl

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

my ($x,$y) = sub () {
    {foo => 1},
    {bar => 2, baz => 3};
}->();

print Dumper $x, $y;

__END__
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Output:

$VAR1 = {
          'foo' => 1
        };
$VAR2 = {
          'bar' => 2,
          'baz' => 3
        };
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