B would be the correct answer, however I understand your confusion.
This sentence is phrased in a strange way, and although it is correct, it feels uncomfortable.
They are saying that Miss Li didn't do anything wrong yesterday, and it is implied that she was blamed for whatever she did by you.
Therefore they are telling you that you should apologize to her.
If you wanted to try and frame this same sentence with the other options you could say:
Miss Li was innocent yesterday, I think you should apologize to her.
Miss Li was innocent yesterday, which means that I think, you should apologize to her
Miss Li, whom you should apologize to, was innocent yesterday.
If I was writing this sentence I would have written:
I think you should apologize to Miss Li, as she is innocent of what you accused her of yesterday.