Oh yes, you're right. How about this:

#!/usr/bin/perl
use warnings;
use strict;

open( LIST, "stopwords.txt" ) or die "$!";
my %stopwords = map { chomp; $_ => 1 } <LIST>;  
close LIST;

while (<>) {
   chomp;
   for (split) {
        print unless $stopwords{$_};
   }
}
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