I'm hoping to get some guidance as to what I missed in the module side of things.

First, thank you for contributing to the free software community.

Second, I agree with holli that you should perhaps rename your module so that it contains letters and semi-colons only.

Third, when looking at your code, the thing I would like to see added is tests of the core functionality. E.g. like the one below (I'd create one file for each main function). I was once surprised just how difficult it is to write working code for multiple platforms, given different architectures and endianness.

# 01-yubikey_decrypt.t

use strict;
use warnings;

use Test::More;
use Auth::Yubikey_Decrypter;

my $fulltoken   = "dteffujehknhfjbrjnlnldnhcujvddbikngjrtgh";
my $aeskey      = "ecde18dbe76fbd0c33330f1c354871db";

my ($publicID,$secretid_hex,$counter_dec,$timestamp_dec,$session_use_d
+ec,$random_dec,$crc_dec,$crc_ok) =
Auth::Yubikey_Decrypter::yubikey_decrypt($fulltoken,$aeskey);

plan tests => 8;

is($publicID,        q{dteffuje},     q{Expect publicID eq dteffuje});
is($secretid_hex,    q{8792ebfe26cc}, q{Expect secretid_hex eq 8792ebf
+e26cc});
is($counter_dec,     q{19},           q{Expect counter_dec eq 19});
is($timestamp_dec,   q{49712},        q{Expect timestamp_dec eq 49712}
+);
is($session_use_dec, q{17},           q{Expect session_use_dec eq 17})
+;
is($random_dec,      q{40904},        q{Expect random_dec eq 40904});
is($crc_dec,         q{51235},        q{Expect crc_dec eq 51235});
is($crc_ok,          q{1},            q{Expect crc_ok eq 1});

__END__
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Fourth, in a question of personal preference, I think the yubikey_decrypt subroutine probably would be better off returning a named hash rather than an 8-element list.