I think there are 2 for each one, one during the game and another one in the ending (with your chosen one). You can only get for one gir at a time.
What do you mean?
You need to be more specific, for what I can understand is that you want to get all good ends, but you got a bad scene 2 times, right? The first one you somehow prevented it by reloading a previuos save right? so you didn't get the same scene the 2nd time right?
The 2nd time you got a "bad scene" for which girl was that scene? also this 2nd playthrough, you started it from the very start? or was the mode you unlock when you finish the game once? (it's a new game where you keep your stuff and levels, etc. and you start after you take DiamondCity, but this time you don't get any bad scene).
If you started it from the very beginning then the scene you are talking about is the one with Seria after you take DiamondCity? or which one is it? If it is, then you can prevent it, but i'm not sure how far behind you need to go to prevent it. As far as I know, every time Ares (the protag) is talking with Seria and you need to pick and answer (for example when she ask Ares if he's gonna come back with her to the island after the war), you always need to pick the option where Ares ignores her feelings. But at the same time you need to keep Seria's loyalty at 100. (also you need to keep all the main girls at 100 loyalty).
Anyways I think even if you save Seria after you take DiamondCity, there will always be a bad scene with one of the "secondary" girls (like for example Marion). But from what you said, I'm guessing you don't care about them, right?