Batman: Arkham Origins
For example, I had it on for Deathstroke. I won. I could NOT continue because it never left the remote grapple gun, therefor I could not quit. Since the game Auto Saves after you win, I had to start over as restart from check point only starts you just after the fight - without the gun.
I started over. I got through that part and made it all the way to Copperhead. Forgot the option was on, could NOT finish my fight with her and was left without the ability to locate the Elecrocutioner.
Started over AGAIN!
I love this game, so it's not a problem. I just hate having to play through the prison again!
You are correct though, it does ruin the scripts this is true for Deadshot as well.