Visible crew/equipment: When Agent Kay is in the elevator with the little worm dudes he swings down and starts shooting at the robot. When he swings down you can see the safety harness between his legs. (01:02:50)
Visible crew/equipment: When Jay enters the tent in which the small alien craft had landed we can clearly see the camera man in the golden reflection. This happens twice. (00:25:00)
Visible crew/equipment: When Jay is addressing the civilians in the small section of the subway car that is left after Jeff ate the rest, green screens are reflected in Will Smith's sunglasses before he neuralizes them.
Visible crew/equipment: When Serleena kicks Z and sends him flying, the person flying and doing all the flips and jumps for all the scene is a very obvious stunt: Thinner built, much younger and with longer hair. (00:46:25)
Answer: They are extraterrestrials, the fact they are weird gives it away to K now he has been deneuralized. He started to notice them again as his mind is rebooting.
lionhead