Thanks ikegami, I just needed to check the variables. This fixed it: 
use strict;
use warnings;
use List::Util 'shuffle';
while (<DATA>) {
    my @newline = split(/\b/);
    for my $word (@newline) {
        my $first = "";
        my $rem = "";
        my $middle = "";
        my $last = "";
        ($first, $rem)  = split /(?<=\b\w)/, $word if $word;
        ($middle, $last) = split /(?=(\w'\w+|\w)$)/, $rem if $rem;
        ((length $middle) == 2) ? $middle = reverse $middle :
        ($middle = join "", shuffle(split //, $middle)) if $middle;
         print "$first" if $first;
         print "$middle" if $middle;
         print "$last" if $last;
    }
}

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In reply to Re^2: unititialized value warning by wrinkles
in thread unititialized value warning by wrinkles

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