Translation:Who was your sister talking to on the telephone?
I suspect you are a native speaker, so this comment really isn't for you, but for any non-native who might read this.
Not actually grammatically correct. The words "with" and "to" are fulfilling the same rule here and one of them should be removed. Since "with" and "to" mean the same thing in this context, it would be wrong to say "With whom was your sister speaking with on the phone?"
"With/To whom was your sister speaking on the phone?" is fine, with the second with/to removed. "Who was your sister speaking with/to on the phone?" is grammatically incorrect, but is the way that nearly every English speaker would say this.