These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Soup-spilling scene. First, the soup itself, descibed as "greasy fluid". Second, Claggart's reaction: "Pausing, he was about to ejaculate something hasty at the sailor, but checked himself, and pointing down to the streaming soup, playfully tapped him from behind with his rattan, saying in a low musical voice peculiar to him at times, "Handsomely done, my lad! And handsome is as handsome did it too!"" (Emphasis mine; if this is not subtext, nothing is.)
"Jemmy Legs is down on you." Even the old wise guy knows it.
"To be nothing more than innocent! Yet in an aesthetic way he [Claggart] saw the charm of it, the courageous free-and-easy temper of it, and fain would have shared it, but he despaired of it."
"When Claggart's unobserved glance happened to light on belted Billy rolling along the upper gun deck in the leisure of the second dog-watch, exchanging passing broadsides of fun with other young promenaders in the crowd; that glance would follow the cheerful sea-Hyperion with a settled meditative and melancholy expression, his eyes strangely suffused with incipient feverish tears. Then would Claggart look like the man of sorrows. Yes, and sometimes the melancholy expression would have in it a touch of soft yearning, as if Claggart could even have loved Billy but for fate and ban."
Designated Hero: Captain Vere. We're supposed to feel sorry for him and pity the terrible moral dilemmas he had to face. But wait a sec. Those dilemmas arose out of the paranoid, violent, and corrupt atmosphere on-board the Indomitable, in particular the bullying behavior of the officers. It is Captain Vere's job to keep the officers in line, but he never says a word against them. The awful situation on board the Indomitable is his fault because he was either too dumb to notice the officers' cruelty, too weak to stop them, or he genuinely thought cruelty was the best way to run a ship. Why do we feel bad for him again?