Caliban's power of detecting those with the mutant gene was one of his strongest abilities, yet it didn't allow him to detect humans in any way. So he was completely unaware of any intruders into the sewers. When Apocalypse saw fit to genetically enhance Caliban, he never altered this power, or enhanced Caliban's senses either. He was however given plenty of combat abilities and the enhanced strength to dish out damage to his opponents.
Seeing Logan rip out his claws and go on edge, put Caliban on alert also. He turned to see around himself better, and spotted at the edge of his vision green lights swishing back and forth in the tunnel. Danger!
"Morlocks Gone, Hiding! All that is left is Caliban!"
Caliban debated how best to handle 'human' intruders to the Morlock tunnels. In the weeks he has been here, alone, he knew the states of the tunnels and twisted passage ways in the city below. If he had to hide, he knew the best places. If he had to flee, the same. Fighting, he knew the best places for that as well.