I have trouble disconnecting myself from what I'm reading too. It's why I don't read dark stories and sometimes (silently) quit fics in rage or revulsion when I strongly dislike whatever I just read. I know I have anxiety, but I'm not sure if that's related.I really don't know why this happens to me or why I have such physical reactions to this kind of thing. Like a really bad case of stomachaches and sometimes makes my head feel light.
As for pet peeves, one fandom I'm interested in seems to have a running theme of whether it's ok for superheroes to kill. Unfortunately, most of the stories with this theme handle it badly. One story I read had the hero ruminating over how he could never support villains being killed when there was a chance that they could be redeemed and some of them had bad childhoods. This would have been more sympathetic if a baby hadn't died earlier in the chapter because of a serial arsonist that had broken out of prison yet again. The hero didn't even take that death into consideration for his internal debate.
Another fic might have a different hero being shown as obviously correct for being willing to kill villains. However, the author will then ignore the repercussions that killing villains should have. A villain who knows that the hero is willing to kill is likely to take more drastic actions than when they're dealing with a hero they know won't kill them. The villain is not going to just continue their routine and let themself be killed.
If stories insist on addressing this issue, I'd prefer for it to be shown as a complicated issue with various heroes taking different stances. It doesn't have to be treated the same as the author's real-world beliefs because the real world doesn't have superheroes and supervillains. The vast majority of people sent to prison in the real world do not break out of prison and commit terrorist attacks.