The most obvious choice is the AR scene with Spike. It just doesn't make sense. The writers had his character come exceedingly close to the moral event horizon (the point when a character become irredeemable for the audience) yet the very next season they expect the audience to feel great sympathy for Spike and almost act as if the AR scene never happened. JM's talent is the only thing that made it work, because if it had been in the hands of a lesser actor, Spike's arc would've crashed and burned in season 7.
Although I did feel that 'Oh no' when Spike tried to rape Buffy it was an important moment for the character's overall arc and in making it clear to the audience that he wasn't a special snowflake, drawing blunt attention to the limit on his capacities when unsouled. As
@WillowFromBuffy says, his perceptions of what was acceptable in relationships was flawed whilst soulless so it didn't feel out of character for him to fail like this and I think keeping the overall verse distinction between souled/unsouled intact was important/needed.
Spike thought that he could walk the line and be what Buffy needed and he could promise her that he wouldn't hurt her. Then we have the attempted rape which taught him that he couldn't be reliable like that. We see why in how confused he is in the crypt afterwards, about why he even cares, why he didn't do it. He doesn't have the moral boundaries to be good for Buffy at that point. The struggle between monster and man had to be something that he
couldn't manage without the soul. His story falls in line with the verse if he
can't just choose to be good as a souled person can. Like with Angel, his soulless actions, all the murders/rapes etc that he had already done, had to be things he didn't really care about, didn't have the capacity for a moral choice over to feasibly give him any true distinction and separation from his evil past. So for me there wasn't anything to make him more irredeemable than all the awful things we've already seen him do, that we've heard about, or that we've seen in the flashbacks, just the same as it has been for Angel. Granted, it was more
difficult for the audience to forgive him for something they've witnessed. Especially something acted against a main character, and the lead after all. But it isn't actually 'worse' than things we know he/Angel have both done in their pasts unsouled.
Season seven dealt with the onward story for Spike, the attempted rape didn't get explored perhaps as much as some would have liked, but drawing that stark line between souled/unsouled is supported in the series and Spike was shown to struggle with his soul/guilt and that was raised between him and Buffy several times earlier in the season. But S7 was about that onward movement, about strengthening and supporting, about overcoming your weaknesses and being strong, being a hero. Empowering each other. I agree JM is very talented and that is definitely one of the main reasons Spike is so great.
Jonathan joining the trio. It was disappointing to me, I felt he owed Buffy more than that and should have known better. Actually, let me rephrase. It wasn't joining the trio that bothered me, cause that makes sense for him as a character. What upset me was Jonathan going along with kid napping and attempted rape of Katrina. I don't see how he didn't realize what he was doing was rape and I'm very disappointed that he didn't do more to stop Warren. I feel like that was exceptionally dark for his character and to me it didn't make sense.
Jonathan is one of my favourite characters, I love the coherency of his arc through the series and I was really disappointed too when he didn't step away from the Trio earlier. I agree it was in character for him joining them and there was certainly the earlier indication in Superstar that he was capable of distancing himself from his actions somewhat. Including even that his spell coerced the twins to being with him, because although it was their choice
he knew it was under false pretences and the spell manipulated people's opinions/thinking. But what was happening with Katrina was far more stark, it was tough to see him having gone that far and not step away sooner.
Angel is one of my favourite characters, I love the complexity and struggles he has. He often falls to repeated hubris in his stories but none of them frustrated me like the ending to AtS 5. It works if looked at in quite a dark way that is still about Angel's struggle and disconnection from his path. But that sense of 'glory' in the final fight I found pretty awful. I agree with
@flow about the disappointment in him killing Drogyn to keep up the pretense of being evil. It was just compounded for me ten fold in him then leading people to make a futile grand gesture rather than continuing the more difficult fight on the ground level that he had started with. The fact that he lied to the group that he was going to be taking out Sebassis when he
knew that he had already set him up to be poisoned by feeding from his slave and he was actually going to try and take out Marcus really frustrated me on the back of him having altered everyone's memories and lied about his reasons for joining W&H in the first place. It just didn't feel that he had learned anything in the season and I really couldn't see it as a positive ending. I don't think that it is as problematic within his overall path, it wasn't out of character, but it felt a very negative moment for the character on its own to me.