I’m so sorry this is hurting you so much. But, yes, following your mother around and invading her privacy isn’t appropriate. As you pointed out, the situation isn’t simple. It sounds like your parents have tried hard to make the best of a situation and to put you and your sister first. It may be that now that you are older, they are starting to think about themselves a bit more. That isn’t necessarily right but it is understandable.
I see you trying hard to be fair. On the one hand, you understand that your mother may have reasons for what she is doing. On the other hand, the little girl inside of you can’t stand it that the family may be shattered.
No, you should not be the one to tell your father and sister. The loving thing to do would be to quietly and privately tell your mother what you think you know. There’s always the possibility that you have misconstrued the situation. It may be that your parents have an understanding with each other that you don’t know about. Before you do any “confronting,” you need to just share your thoughts and feelings. You can certainly tell your mother how confused, hurt, and scared you are. It might also be helpful for you to tell her that you feel like you are in the middle, that you love both your parents, and that the situation makes you feel like you are betraying your dad and sister. Ask her to get you out of the middle by talking with your father.
Then leave it to your parents. You are not a detective. You are not a counselor. You are not a judge. Your parents need to decide if and how they want to be married. Those are your parents’ decisions. You can tell them how you feel. But their feelings for each other are between them.
Your parents are each decent people who have done their best for a long time. They both love their girls. They’ve raised a daughter as sensitive and caring as you are. Although this is likely to be a difficult time for your family, it sounds to me like things will eventually be okay.
I wish you well.