I have three big ones
1. Character trades quest minor progress for a major side quest. I find this enraging because the came typically frames it as them being an okay person. In Fallout 3 I have wandered into the world looking for my father who has left for unclear reasons, is in uncertain danger, and may be getting further and further away. Three Dog could help me out by saying the words "rivet city" instead he asks you to do a quest for him first. In New Vegas, Honored Hearts DLC your caravan is butchered and your lost in the grand canyon, you need a map to navigate the crags and get back home, a quick look with a paper and pencil would be sufficient. Josh Graham and Daniel hold this information hostage, keeping you trapped in unfamiliar country until you do about a hundred quests for them. In Kingdom Come Deliverance Melichar refuses to let you speak to a prisoner until you cure a plague. You have been ordered to your lord to speak to the prisoner and if you dawdle there may be a massacre. This one gets a little bit of a pass because the prisoner has the plague but Melichar flat out refuses to let you see him.
In each situation I killed everyone involved and was treated as a bad guy. Note that I never wanted anything from these characters, we were not exchanging equivalent favors. I needed directions, directions, and a guy to open his barn. Actively harming my interests is not a friendly act, if I am a good character stopping me from achieving my goals makes you a bad guy. I subsequently hated each of these characters regardless of how well they were written or relatable they were because you introduced them as massive pricks.
2. Problems that exist because my character is a big dumb dummy. This can be getting captured, defeated, or outsmarted in a cutscene or just your character being blindsided by something that you immediately picked up on as a player. There are too many examples, this is a favorite of terrible writers. If you need the character to be vulnerable snatch control from the player and make them act like an idiot. I think Hitman Absolution may be the best example. 47 tries to murder a bodyguard who is basically an oil tanker made of meat. He is easily overpowered and instantly knocked unconscious. This is a series where half of the gameplay is about not killing bodyguards in fact killing bodyguards is the mark of a poor player. If you were going to kill him why not shoot him in the back of the head? Why not do one of a hundred things that aren't stupid? Because then it would make less sense that you were easily defeated. In KCD you question someone who is clearly lying to you and acting suspiciously, you have no option to call him on it or tell somebody to watch him and he runs away before you find evidence that confirms he knows more than he was saying.
This isn't necessary and some games actually do it right. Batman: Arkham Asylum the joker escapes and initiates his plan despite the player character behaving reasonably and intelligently. In that cutscene you think "wow the Joker's dangerous" not "wow I am playing as a moron."
3. Unanswerable dickery, a character who repeatedly antagonizes you that you have no recourse against. In Skyrim Maven Blackbriar insults, belittles, and threatens the protagonist who may be the worlds deadliest warrior, greatest assassin, and most powerful mage who in their spare time screams at dragons until they die. You never get to do anything about it and she's mechanically unkillable. In KCD after tending to the sick you're sent to jail (by a single guard) for requesting someone supply your former neighbors and victims of war with enough food to eat. For me this happened while my sword was literally stained with the blood of the last twelve unfortunate motherfuckers who tried to arrest me, seriously I got stopped by guards on my way to the quest and an actual trail of bodies led to the quest marker. The louse in question is unkillable.
There are games where a character messes with you and then anticlimactically disappears but I think this is a bigger problem in rpgs with an open world. Sure, maybe some characters have to be flagged as essential, if that's the case I think they should have to sob uncontrollably and wet their pants when confronted with violence- if someone has to act out of character and be humiliated for the story to work then why should it be the player?