G'day Marshall,

I added strict and warnings: both missing from your code. I also show assignments to %master_letter_freq and @result: also missing from your code. The remainder is a verbatim copy of the code you posted.

#!/usr/bin/env perl

use strict;
use warnings;

my %master_letter_freq = qw{w 1 h 1 t 1 o 1 r 2 e 1};
my @result = qw{thew trow whew};

RESULT: foreach (@result)
        {
            my %seen;
            $seen{$_}++ for (split //,lc $_);

            foreach (keys %seen)
            {
                next RESULT if ($seen{$_} > $master_letter_freq{$_});
            }

            print "$_\n";
        }

foreach (@result)
{
    my %seen;
    $seen{$_}++ for (split //,lc $_);

    my $no_print = 0;
    foreach (keys %seen)
    {
        $no_print++ if ($seen{$_} > $master_letter_freq{$_});
    }

    print "$_\n" unless $no_print;
}
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Here's the output:

thew
trow
thew
trow
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Please run that code, exactly as is, and report the output.

If you still see "whew" in the output, then there's potentially a bug in Perl. I'm using 5.32.0. What are you using? Post an SSCCE so we can investigate.

If you don't see "whew" in the output, then either the code you're running is not the code you posted, or there's something else going on in the code before this that you haven't shown.

Add code to query every variable before and/or after it changes. For instance, with Data::Dump:

dd \%master_letter_freq;      # <-- QUERY
dd \@result;                  # <-- QUERY
RESULT: foreach (@result)
        {
            print "|$_|\n";   # <-- QUERY
            my %seen;
            $seen{$_}++ for (split //,lc $_);
            dd \%seen;        # <-- QUERY
            # ... and so on ...
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Note the pipe characters (|$_|) that may help to identify whitespace or control characters that aren't readily visible.

If that doesn't help, try (platform-dependent):

./script.pl | cat -vet
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That's something of a last resort, but it may show up something if all else has failed to identify the problem.