Not the most efficient method, but anyway, assuming that both your files contain one word per line, the mistake is here:

WORD:
foreach $word (@data)
{
   STOP:
   foreach $stop (@stopwords)
   {
      next WORD if $word eq $stop; # <---
   }

   push(@lessWords, $word);
}
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Whenever a stopword matches, you should exite the outer loop.

Consider using a hash instead.

my %stops = map {$_,undef} @stopwords;

for my $word (@data)
{
    next if exists $stops{$word};
    push(@lessWords, $word);
}
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