See, this is what riles me up. It's bad enough DC editors apparently don't talk to each other but it seems they don't even edit their own books. Or maybe Batman just can't count. Or maybe the fourth ninja is like invisible-Ninja but Batman can see him because he was wearing his infra-red Bat goggles or some shit like that. Or maybe...maybe...erm, the moonshine he was sniffing made him all drunk and he saw one extra ninja. Maybe.
Nope. No invisible-Ninja. Just bad editing.
From The Resurrection of Ra's Al Ghul hardcover collection by Morrison and Dini.