Effectively, there's an unstated that phrase:
What do you see in her that you find attractive?
It can be used in other situations, with different implicit phrases.
You're eating at Nando's again? I don't know what you see in that place.
I don't know what you see in that place that causes you to eat there so often
You're listening to early Genesis? What do you see in it?
What do you see in it that makes it worth listening to?
(Yes, the expression is also used for things you don't see)
I see you have a full collection of Police Academy. What do you see in those films?
What do you see in those films that makes it worth owning them, and thus presumably re-watching them frequently?
It generally expresses incredulity or scepticism.