"Who is she kissing with?"
Translation:עם מי היא מתנשקת?
I agree. It's just that the Hebrew sentence uses the reflexive form of the verb, which means that the question is about the identity of some person that she is kissing and that person is kissing her back. That is the normal way to express it in Hebrew. You would never say "את מי היא מנשקת" as that implies that that someone is not kissing her back.
In English you would say "who is she kissing?" In a statement it makes perfect sense to say "they are kissing (each other)", but I don't know of a good way to turn that into a question. Maybe "who is it that she and him are kissing each other?"
Anyway, kissing is normally reciprocal in Hebrew, but not in English.