Billy continued to notice Claggart smiling at him and acting nicely toward him. However, there were other indications that Claggart was not so fond of Billy. Upon seeing Billy, Claggart would often have a look of melancholy or sorrow mixed with yearning and at times would show an odd red glint in his eyes. In his innocent ignorance, Billy did not notice any of this.
Claggart tries not to display his inner dislike of Billy, but there are still outward signs of his animosity toward the innocent sailor, which Billy does not notice. It's worth thinking about the fact, though, that a look of "melancholy or sorrow mixed with yearning" and even "an odd red glint" in the eye aren't definitive signs of hatred, and to wonder if the narrator really is reliable.
The ship's armorer and captain of the hold, both messmates of Claggart, also habitually looked at Billy with critical glances, but Billy did not think this was suspicious and his handsomeness and good nature maintained his popularity among most of the sailors on the ship.
Is Claggart turning his messmates against innocent Billy? (Though given later events one might also wonder if Claggart has gotten wind of the after-guardsmen's approach to Billy and therefore suspects Billy of connection to a mutiny, and his messmates therefore suspect Billy too.) Billy doesn't think that his comrades onboard the ship would turn against him, especially as his good behavior and appearance have ensured the goodwill of most of the sailors.
The after-guardsman who had approached Billy in the night behaved kindly toward Billy whenever the two saw each other. The narrator says that readers may think that Billy should have asked the after-guardsman his purpose in asking for Billy's help, or should have asked other sailors to see if he could figure out what was going on. Such questioning, though, was out of line with Billy's nature. Meanwhile, Claggart's hatred for Billy was growing, such that "something must come of it."
Like Claggart, the after-guardsman behaved with a deceptively polite demeanor toward Billy. The narrator sees Billy's innocent nature as determining the course of his actions. By guessing the reaction of his readers, the narrator emphasizes his own role as a storyteller. Once again, such narratorial intrusion may raise at least a partial suspicion in the reader about whether the narrator's story is reliable—because even if unintentional, such narration provides an explanation that may not match up with what the reader would have come to without it. The narrator explains how Billy's silence comes about because of his innocence, but a reader who disregards the narrator might wonder if perhaps Claggart, might see (whether rightly or wrongly) Billy's silence as arising from something more nefarious.