Your match is finding portions of a word: $key =~ /$i/ will match when $key is "elephant" and $i is "a" because "elephant" contains an "a". To match on whole words only, use /b (word boundary - see perlre) before and after your search term:

my %histogram;
my @wordstofind = qw(
  a am an and are as at be been but by can co de do due each
);

while (<DATA>) {
  my @currentline = split;
  $histogram{$_}++ for @currentline;
}

foreach my $i (@wordstofind) {
  while ( my ($key, $value) = each (%histogram) ) {
    if ($key =~ /\b$i\b/) {
      print "Found $key, $value times\n";
    }
  }
}
__DATA__
hello, I am an elephant. I have a long trunk.
[download]

Output:

Found a, 1 times
Found am, 1 times
Found an, 1 times
[download]