while (<WORD>) {
    chomp;
    next if /[^a-z]/; # Lazy way out~
    my @chars = split(//, $_);
    push @{$wordlist{$#chars}}, $_;
}
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You appear to have an off-by-one error where @chars contains the characters from the word in $_ so $#chars will be one less than the number of characters in $_.   Perhaps you meant:

while ( <WORD> ) {
    chomp;
    next if /[^a-z]/; # Lazy way out~
    push @{ $wordlist{ length() } }, $_;
}
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