foreach my $line (@words) {
    $line =~ tr/A-Z/a-z/;
    foreach my $ignore (@ignore) {
      $line =~ s/\b$ignore\b//g;
    }
  }
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Oh, I didn't notice that at the top, you need to change

my @ignore = qq(a and the this i me us our ok abc);
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to

my @ignore = qw(a and the this i me us our ok abc);
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I.e. change qq to qw.

Thanks so much!! After looking at that I slapped myself in the forhead for making a mistake like that, I think this was my major problem all along (oh, I feel stupid). I was wondering why qq() didn't show up as an error but it turns out that's a real command too, go figure :)

Thanks for your help Thelonius and every other monk who hasn't slapped themselves into the next cyberworld from my mistakes.