My all-time hated trope is tsundere characters; I don't get why anyone finds them interesting or entertaining. They act more like mobile drama balls than sympathetic characters. I've wanted desperately for an MC to react to their bullshit with a simple, "Oh, you don't like me? Fair enough, I won't talk to you again," and have that be the end of their relationship until/unless the tsundere actually matures and realizes how much of a pain in the ass they are, but I have yet to see that in any manga. I watched Familiar of Zero, and by the end of the first season, I was hoping that the MC would turn his plane around and strafe all of those assholes before escaping from the hell that they'd summoned him into.
More abstractly, tonal inconsistency. I get light, fluffy manga about, I dunno, a group of otaku in an office falling in love. I get dark, heavy manga about a girl seeking revenge against an emperor who murdered her entire family without understanding the political situations involved. I even get the slow, desperate spiral into doom that Helck and some other manga manage to pull off. But yoyoing back and forth between wacky slice of life romcom antics with a pair of cousing trying to take care of this weird girl they found on a beach, and horrifying scenes of little girls getting their limbs torn off, is fucking awful. Or the random, one-off scene in some power-fantasy monster-of-the-week adventure story where we learn that oh yeah, the government is running a brutal program slaughtering thousands of clones of the main character (who is, of course, a child) and now it's just in the manga's world forever, and the characters just move on. It makes me hesitant to start reading certain genres because of how rife they are with this edgelord shit.
More recently, shit worldbuilding. People have already mentioned status screens, paper thin settings, hideous understanding of morality, and plots that exist only to glorify the MC, but it goes even deeper. Nothing in their worlds make sense. They're not filled with people, they have cardboard cutouts, waiting for the MC to show up and show them how to exist in the world that they've supposedly been living in for millennia. I just read a manga where it was noted that fish was expensive because no one knew how to keep it safe for eating past a few days. Because this was, of course, a medieval world. Meanwhile, we've been preserving meat practically since before civilization existed on Earth!