You actually want:

foreach (@lines) {
  if(/(\w+)\s+(\w+:\w+)\s+(\d+\.\d+\.\d+\.\d+):\w+\s+(\w+)/) {
    $protocol = $1;
    $localAddress = $2;
    $foreignAddress = $3;
    $state = $4;
    print "$protocol, $localAddress, $foreignAddress, $state\n";
  }
}
[download]

This is because if a line fails to match, perl will not reset $1, $2, $3, $4, so they will still have a value from the previous match.

Also, if you are not going to use the @lines array for something else, it's much more memory-efficient to combine the loops like this:

  open NETSTAT, "$program|" or die "Cannot open netstat $!\n";
  while (<NETSTAT>) {
    if(/(\w+)\s+(\w+:\w+)\s+(\d+\.\d+\.\d+\.\d+):\w+\s+(\w+)/) {
      print "$1, $2, $3, $4\n";
      # protocol, localAddress, foreignAddress, state
    }
  }
[download]