I'd replace the whole inner loop with next if grep {$seen{$_} > $masterLetterFreq{$_}} keys %seen; giving:

use strict;
use warnings;

my @result = ('thew', 'trow', 'whew ');
my %masterLetterFreq =
    ('w' => 1, 'h' => 1, 't' => 1, 'o' => 1, 'r' => 2, 'e' => 1);

for my $word (@result) {
    my %seen;

    $seen{$_}++ for split //, lc $word;

    next if grep {$seen{$_} > $masterLetterFreq{$_}} keys %seen;

    print "$word\n";
    next;
}
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which avoids the goto label nonsense and avoids silly flag twiddling. Note that this code often generates a warning, but I haven't seen it print 'whew '. There is something more going on in your real code that gets 'whew' printed, but we don't have that code or a sample we can run to reproduce that error.