I assume that you are talking about the part in the story where the narrator has gone to see the signalman for the second time. At this point, the signalman is telling the narrator about the (he thinks) supernatural things he has seen. When he does this, the narrator tries to calm him down by providing explanations of how the signalman might have been mistaken.
What is going on here is that the narrator is representing an enlightened person who believes in science and not in the supernatural. Here is a quote that shows what the narrator is trying to do:
I showed him how that this figure must be a deception of his sense of sight; and how that figures, originating in disease of the delicate nerves that minister to the functions of the eye, were known to have often troubled patients, some of whom had become conscious of the nature of their affliction, and had even proved it by experiments upon themselves. "As to an imaginary cry," said I, "do but listen for a moment to the wind in this unnatural valley while we speak so low, and to the wild harp it makes of the telegraph wires."