I already did:

open( LIST, "stopwords.txt" ) or die "$!";
my @stopwords = <LIST>;
chomp(@stopwords); # <- was missing

my %stopwords;

# Create an element in the hash for each stop word.
undef @stopwords{@stopwords};
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or using less memory:

# Create an element in the hash for each stop word.
my %stopwords;
open( LIST, "stopwords.txt" ) or die "$!";
while (<LIST>) {
   chomp;
   undef $stopwords{$_};
}
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Update: Added chomp.