You can just refine the regex within the grep. In this case using the block form of grep is I think better... If the stop word is either at the beginning or at the end of the "$word", then it is a match.

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

my @words = ("of the blue","the blue of","out of blue");
my @stopwords= ("a","the","of");

foreach my $word (@words)
{
   if (grep{$word =~ /^$_/i or $word =~ /$_$/i}@stopwords)
   {
      print "Stopword $word discarded\n";
   }
   else
   {
      print "$word is not a stop word\n";
   }
}   

__END__
Stopword of the blue discarded
Stopword the blue of discarded
out of blue is not a stop word
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