#49 is stunned to see there's another one of him. But if an army of Crooze's took over the planet (Longo's screaming for a prequel right now) wouldn't they have all seen one another and realized that they were clones? If they remembered their humanity like 49 did, wouldn't they have stopped and wondered why they were killing everyone, much like how he did when he realized that drones were shooting on survivors?

Personally, it was one of those "Whatever, I'll go with it" issues for me but I think it's pretty hard to explain the logic behind it. Similarly, it was kind of silly that the way to get around the drones shooting at the Skavs was that they just dressed up like animals, which the drones wouldn't shoot. You'd think you'd reprogram them to kill everything since you were going to kill them anyway once you took all of the water from the planet.