This is a big one. For most of the comic, the only things that die are the nameless, possibly-non-sapient Underlings. (And even then, killing that first Imp over a stuffed rabbit bothered me. It didn't actually seem dangerous, just making comical attempts at intimidation.)
And then the parents die. No fanfare, no epic martial arts battle. And I think: what was the point? Why bother bringing the parents into the game, hilarious though DAD's antics were, if they don't do anything important except die? Such passive pieces don't deserve that much time and buildup, and additionally, MOM still hadn't explained her connection to Skiaianet, or what Skiaianet is. It was very unsatisfying. (Not least because there was no awesome fight scene to mitigate it.)
I had basically the same problem with the trolls dying. What was happening? Why would you waste so much time briefly showing characters you're just going to kill? And why is Gamzee even able to kill Eqiuus, let alone an enraged Nepeta, without being reduced to thematically-appropriate confetti? And I'd sort of liked Eridan, so him suddenly turning Murderous Yandere felt unwarned and unwarranted. Sollux asking if the voices being silent means they doesn't have to die anymore was deliciously tragic, though, and Aradia's speech to one of the dead Daves was great. "He is not yet comfortable with his own mortality. But people like us have to be! We must be prepared to die a thousand deaths before our journey's done. The master we serve demands it."