#Hamming distance
sub hd {
   my ($d1,$d2,$bits) = @_;
   $bits ||= 8;
   my $diff = $d1 ^ $d2;
   my $count = 0;
   for my $b ( 0 .. $bits-1 ) {
      my $mask = 1 << $b;
      ++ $count if $diff & $mask
   }
   return $count
}
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When I run your subroutine I get the warning message:

Argument "^C" isn't numeric in bitwise and (&) at -e line XX.

That message means that $diff is a string and $mask is a number.    You can use the bit-wise operators like & on two strings or two numbers but not on a number and a string.

perl provides a way to count bits in a string using the unpack function.