Anyway, the question...this is hard to answer, because I can't really think of any one single thing that made me dislike a game. I mean, there's plenty of stuff I might dislike, but I'd like to think those aren't petty reasons, and even if they were, it's not a case of "I dislike this thing, ergo I dislike the game."
The closest things I can think of are:
-Gears of War: Judgement
So, in the game, you can take on extra difficulty settings, like, decreased vision, or no regenerating health. The in-universe explanation is that these factors were sealed by the COG. However, why? Why cover up reports that stated that Kilo Squad was so tired they couldn't regenerate health, or, visibility was low at this point in time? I can understand some, like a Hammer of Dawn strike going off-course, but the in-universe explanation makes no sense for what's otherwise a gimmick.
-Half-Life 2: Episode 1
So, I'm not a Half-Life fan, but of all the things that I dislike about Ep. 1, one of them is at the end. Towards the end, when you're in the train yard, helping refugees escape, you see a group of Combine soldiers coming towards you. As City 17 is on the verge of being destroyed, my first thought was "hey, maybe they're trying to escape with us. Maybe the game will try and introduce moral complexity of people who turned their back on humanity, but now want to join the Resistance. I mean, up till a few hours ago, there was no reason to suggest that humanity had any hope against the Combine. Maybe this is going to lead to something interesting...
...or not, as they just start firing, and I'm forced to kill them. Yay...
-Mass Effect: Andromeda
The kett. Just the entire way they're handled. I'm calling this petty because the game's under no obligation to treat them and the angara in a given way, and you could say that I'm setting a double standard for the lack of moral ambiguity in ME1. But you know how I feel about the kett on the "currently playing" thread, and, yeah. I still think the game's narrative shot itself in the foot here.
-Sonic Chronicles: The Dark Brotherhood
This is the closest example that meets the criteria. Now, I really dislike this game, even if there's far worse STH games in the series. That I dislike it this much because of its story/lore is arguably weird, because I've let other games get away with worse, but that this was from BioWare after ME1, coupled with Ken Penders being a douche, made it all the worst. But what got me to stop playing after all these frustrations was towards the end where you see two gizoids show up. Yep, turns out Emerl wasn't the only gizoid, and they're just off the assembly line. Because that totally doesn't undercut the plot of Sonic Battle at all (sarcasm). At this point I gave up, because I couldn't take the constant barrage of nonsense anymore. More fool me, because turns out I was actually quite close to the end.
-World of Warcraft
I'll always have some dislike for this game, because no matter its quality/lack of it, its mere existence is part of the reason why we'll almost certainly never get a Warcraft IV.