Spoiler warning, as people are obviously going to tell you about the games.

So we know that more and more games are coming out with moral/choice parts of their stories which affect it. But some of those are either the wrong decision or maybe not the nicest. What are the ones you think are the worst to make (and therefore didn't) or maybe you did, whether you agreed with the choice or not?

For me is was Mass Effect 3, shooting Mordin Solus in the back. I had 4 main characters, a first playthrough one, a paragon guy, a renegade and an Shpeard who was useless and got most of his team killed. Out of every decision and choice in the game, the renegade Shepard was at least a good person, doing it for the right reason, they were just a dick. But that one moment, actually going through with it, shooting Mordin was really hard and I'd say one of the worst to actually do. It changed Shepard into a renegade doing things their way to get the right results into a murderer to do it. Then, if I recall, there is a scene where Shepard straight up lies (or omission of truth basically) about what they did to everyone else.

Yours?

I entered Honest Hearts (Fallout New Vegas) with the 'wrong' apparel and everyone was attacking me, by the time I realized my mistake I had no desire to restart so I never played it 'properly'.

In Final Fantasy Tactics, there's two successive battles before you fight Velius. You're given the option to save your game in between the two fights, which I did. The problem is that the fight against Velius is fucking brutal. I got my ass handed to me over and over and thanks to saving right before the fight, I didn't have the option to go back to the world map to level. I thought I'd have to start over from the beginning of the game (which would have meant many many hours lost) but I finally managed to win with some tweaking of my party and a lot of luck.

On the moral level, I don't feel that I've ever made a "wrong" choice in a game. They're games, after all. So, nobody actually does. We just choose how we experience the story. I just don't see any wrong in there.

In a stupid move that screwed up my gaming experience sense, there are too many to count. Most of them would probably be in games from the 80s and 90s, where you ran into a lot of situations like TruckOSaurus describes above. And, of course, everyone that was gaming back then knows that "oh shit, I forgot to save for four hours" feeling that piles on right after you get your ass kicked in a boss fight.

I don't think I ever felt bad in a moral sense about a choice I made a video game. they're just games, nobody actually dies. We're just exercising a little bit of control over how we experience the story. I don't feel bad about any of that.

In a stupid decision that screwed up my gaming experience sense, there have been a lot. Then there's the "oh shit, I forgot to save for 4 hours" feeling that piles on right after you get your ass kicked in a boss fight.  Anyone that was gaming back in the eighties and early nineties knows that one. I did that a lot.  I don't know that I've ever felt so frustrated as I have in some of those moments.

I recently killed the level 1 baby armu in XC2.
I only regret it because of loosing the benifits I would later get from it.

Assassin's Creed Odyssey.

The very first moral choice you get to make is wether to kill a sick family that isn't recovering. They looked fine and they said they were getting better, so I killed their would be killers and they were free. Turns out they were sick with the Plague of Athens. Now the intro Island is covered in a eerily thick fog with dead bodies littering the towns and villages. Perpetual rain as well. I could have stopped the Plague of Athens from spreading, now it will effect the rest of the games regions by end game.

I player through the entirety of Final Fantasy VIII without draining magic or upgrading my weapons. I just GFed everything to death and healed as needed. Once you get to disk 4 however, this strategy no longer works and limit breaks and junctioning magic is key. Unfortunately without ever upgrading my weapons, I had nothing but the first limit breaks and weak attack power. You also get locked out of towns on disk 4, so there was no way for me to upgrade my gear. My save file essentially became unplayable and never really finished the end of the game.

I was young and new to JRPGs...don't judge me!

Rushed in Red Dead Redemption II because the spoilers were everywhere

Seems I read the OP too fast and my answer was not exactly what he asked for.

So I'll add another reply: I harvested EVERY. SINGLE. Little Sister in Bioshock because I wanted all the ADAM I could get.