Wayne's warning acted as the tipping point in that strange situation. Khan still couldn't understand what was happening, but his alert instantly reached its highest level.
Both of Khan's hands went on the control desk while a storm of thoughts and simulations filled his brain. Liiza also made herself as small as possible on his lap, giving him room to work while warily inspecting her surroundings and preparing for the worst.
That abrupt development couldn't have been stranger. Khan was inside his ship, and its many channels into the universe were closed, so he shouldn't have been able to sense much past the hull.
However, the ship was small, and Khan's perception encompassed it in its entirety. He even perceived details from inside Zalpa's living quarters despite all the protections she had placed.