I suspect you are reading a file created with \r\n (carriagereturn-linefeed) line endings (e.g., on a Windows system) on a system (e.g., *nix) that uses \n (linefeed) line endings. On the reading system, the line-feed is chomp-ed off leaving the carriage-return. This can be simulated with something like:

Win8 Strawberry 5.8.9.5 (32)  Fri 09/03/2021 23:52:22
C:\@Work\Perl\monks
>perl

use strict;
use warnings;

use Data::Dump qw(dd);

my $data = <<"EOD";
AA\r
AAH\r
AAHED\r
AAHING\r
AAHS\r
AAL\r
ZYTHUMS\r
ZYZZYVA\r
ZYZZYVAS\r
ZZZ\r
ZZZS\r
EOD

open my $fh, '<', \$data or die $!;
my @words = <$fh>;
close $fh;
dd \@words;

chomp @words;
dd \@words;

print "@words\n";

^Z
[
  "AA\r\n",
  "AAH\r\n",
  "AAHED\r\n",
  "AAHING\r\n",
  "AAHS\r\n",
  "AAL\r\n",
  "ZYTHUMS\r\n",
  "ZYZZYVA\r\n",
  "ZYZZYVAS\r\n",
  "ZZZ\r\n",
  "ZZZS\r\n",
]
[
  "AA\r",
  "AAH\r",
  "AAHED\r",
  "AAHING\r",
  "AAHS\r",
  "AAL\r",
  "ZYTHUMS\r",
  "ZYZZYVA\r",
  "ZYZZYVAS\r",
  "ZZZ\r",
  "ZZZS\r",
]
 ZZZSYVAS
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