Ooops I did not check the code I posted, again. I really need to stop doing that. Here is what the program should have looked like.

use v5.16;
use warnings;
use autodie qw( :all );
use utf8::all;
use File::Slurp qw( read_file );
use Regexp::Assemble;
use Benchmark qw( cmpthese :hireswallclock );

my %seen;
my %seen2;

my $fname   = 'dracula.txt';
my $content = read_file($fname);
$content =~ tr/!"#$%&'()*+,\-.\/:;<=>?@\[\\]^_`{|}~/ /;

my @patterns = read_file('sample_patterns');
chomp @patterns;
my $regex = join '|', map {quotemeta} @patterns;
$regex = qr/\b($regex)\b/ixms;

my $regex2 = Regexp::Assemble->new->add(@patterns);
$regex2->anchor_word(1);
$regex2->flags('ixms');
$regex2->re();

cmpthese(
    -5,
    {   
        'one' => sub {
            $seen{$1}++ while $content =~ /$regex/g;
        },
        'two' => sub {
            $seen2{$regex2->mvar(1)}++ while $content =~ /$regex2/;
        },
    }
);
[download]

I understand now why it was acting the way it was.