You're still pushing $word onto @lessWords regardless of the match. Simple fix:

foreach $word (@data)
{
        my @arr=split(/ /,$word);
        WORD:
        foreach $a (@arr)
        {
           foreach $stop (@stopwords)
           {
              next WORD if $a eq $stop;
           }
           push(@lessWords, $word);
        }
}
[download]

using a hash for @stopwords would make this code simpler and faster, though. There are some examples in this thread somewhere.

update: the above code is still buggy. See below for a much simpler version that should work.