When you're invisible, it doesn't really matter if it's light or dark, right? No one can see you either way. But in the first few chapters of The Invisible Man, the villagers in Iping only seem to see things in dim lighting. For instance, Mrs. Hall sees that the Invisible Man has a gigantic mouth (really, just a hole in his bandages), but she's not sure of what she saw because "[e]verything was ruddy, shadowy, and indistinct to her, the more so since she had just been lighting the bar lamp, and her eyes were dazzled" (2.5). Similarly, Mr. Hall goes to check on the Invisible Man and thinks he sees a handless arm, but isn't sure because the room is dim (3.8).
What do these moments of darkness have in common? Well, when it's dark, there's uncertainty.
People are never sure what they've seen – they think it's because the lighting is bad, but really, it's because they're looking at an invisible man. So could this darkness represent an ignorance on the part of, well, everyone? Because modern science was just starting to develop in the late-nineteenth century, people were still in the dark about most of it and Wells seems to be pretty aware of this.