There is nothing wrong with your code. You are extracting all words and matching all badwords. I slightly adapted your code and added some print-statements to see what happens:

use strict;
use warnings;

my @badwords = qw/crud crap poo wanker/;
while (<DATA>) {
    my $line = $_;
    my $plainline = $line;
    $plainline =~ s/["'.,!?:;\-()[\]{}|\\\/]/ /g; #replace all punctua
+tion with a space
    my @sentence = split(/ /,$plainline);
    print join '|', @sentence,"\n";
    foreach my $word (@sentence) {
        chomp($word);
        print "\tChecking *$word*\n";
        my $whichword = 0;    # to track which badword was found
        foreach my $badword (@badwords) {
            if (lc($word) eq $badword) {
                print "\t\tFound $badword\n";
                #my $newword = replaceword($whichword); #get a cleaner
+ word to replace the naughty word
                #$line =~ s/($word)/$newword/i;
            }
            $whichword++;
        }
    }
    #$cleanbook .= $line;
}

__DATA__
"Wanker!" said I.
"Crap," says Travis.
This is horse poo. Poo, I tell you!
"Poo upon all the crud and crap the wanker could see."
[download]

And the output of this is:

|Wanker|||said|I|
|
    Checking **
    Checking *Wanker*
        Found wanker
    Checking **
    Checking **
    Checking *said*
    Checking *I*
    Checking **
|Crap|||says|Travis|
|
    Checking **
    Checking *Crap*
        Found crap
    Checking **
    Checking **
    Checking *says*
    Checking *Travis*
    Checking **
This|is|horse|poo||Poo||I|tell|you|
|
    Checking *This*
    Checking *is*
    Checking *horse*
    Checking *poo*
        Found poo
    Checking **
    Checking *Poo*
        Found poo
    Checking **
    Checking *I*
    Checking *tell*
    Checking *you*
    Checking **
|Poo|upon|all|the|crud|and|crap|the|wanker|could|see||
|
    Checking **
    Checking *Poo*
        Found poo
    Checking *upon*
    Checking *all*
    Checking *the*
    Checking *crud*
        Found crud
    Checking *and*
    Checking *crap*
        Found crap
    Checking *the*
    Checking *wanker*
        Found wanker
    Checking *could*
    Checking *see*
    Checking **
    Checking **
[download]

Maybe the error is in your replaceword sub?

As you see, you have lots of empty items in your wordslist since you replace punctuation by spaces and then split on spaces, effectively dropping all spaces but making a lot of empty "words".