"Why are you sitting while your father is working?"
Translation:Baban çalışırken sen neden oturuyorsun?
"işlerken/işlemek" means processing which makes the sentence you suggest an incorrect translation for the sentence above. Also, the father would have to be processing something however there isn't an object being processed in your example, so it doesn't work for that reason as well. Unless the father is a computer or something? :)
You are possible confusing Azeri with Türkisch which are very close.
Is "neden sen oturuyorsun" wrong? I'm never sure where you can and cannot place the question word.