Seriously, I don't find her question so weird. Baba is behaving like an ass. He is not being clear about anything. He keeps asking her to forgive him, but forgets to tell her that he loves her and wants her and what he did was a mistake he will never make again because he knows that she loves him too and that he trusts her.
First, he tried to push her towards Dhruv and now feels jealous and pouts even though he knows that Nandini considers Dhruv her friend. He knows it too. He himself tried to make it more, to push this more-than-friends thing on Dhruv and Nandini.
He said to Cabir that he knows that she has no feelings for Dhruv.
Only if Baba would man up and tell her, put it into straightforward words that she herself uses all the time, 'I am in love with you ..'.
At this point if she looks at Dhruv and wonders, this guy is so simple, this guy is so straightforward, this guy looked at me and told me that he loves me.
Why did I fell in love with his friend? Why not him?
It is all right. She is human too ... She can wonder how different things would have been if it was Dhruv for her.
But she knows that Manik is the one for her, at this point where he has pushed her, if she is frustrated and wonders ... IT IS FINE!