In "Lord of the Flies", what is the significance of "the darker smudge that had been the fire"?

This particular phrase is a bit of imagery meant to imply, before we are told, that the fire has gone out, perhaps as a way of sharing with us that momentary anxiety the boys must feel when they realize this. It can also be interpreted as something of a judgment of the quality of the fire and the boys' efforts.

At this part of the story, the twins, Sam and Eric ("Samneric") have been tasked...

This particular phrase is a bit of imagery meant to imply, before we are told, that the fire has gone out, perhaps as a way of sharing with us that momentary anxiety the boys must feel when they realize this. It can also be interpreted as something of a judgment of the quality of the fire and the boys' efforts.

At this part of the story, the twins, Sam and Eric ("Samneric") have been tasked with caring for the fire. Unfortunately they are so inseparable that they struggle to accomplish two individuals' worth of responsibilities; in fact, Piggy later chastises Ralph for always counting the twins as a single person when it came to the delegation of duties, rather than two people. Here, we are told that they could never accomplish anything if it required them to act as individuals, and so they simply didn't do their job; they both went to sleep, and allowed the fire to go out. 

The choice of the word "smudge" implies that the fire is small, meager and weak; that it barely left a mark behind indicating its existence. This suggests that the boys, despite being able to create fire, haven't truly mastered it. As it turns out, the fire is just hot enough that the twins are able to safely rekindle it, but Golding's choice of words and tone in this section are meant to imply that any self-satisfaction the boys feel is forced and fake; we, and they, should feel relieved that their mistake was correctable.