"Σε ποιον μιλάς;"
Translation:Who are you talking to?
That translates to "Με ποιον μιλάς;", not "Σε ποιον μιλάς;"
Εven though the difference is very small, it's there. In the first case, it's implied that there is some sort of response or conversation between two speakers, while the second one doesn't imply a thing. You might be talking to someone without them even listening to you.
A lot of English grammar has been simplified but there is one rule that I'm afraid is still around. That is the use of "whom" after a preposition (other uses of whom have been lost).
So, here you would need "To whom are you talking." which is already one of the accepted translations. It's also mentioned on this page.