yup, both can be used, but in different situations: (Class room is too loud, car won't start, you feel sick but you don't know why) ---> "what is the problem?" vs. (somewhere in the class room, something is making a sound, some part of the car seems to have a problem, a part of your body hurts) ----》 "where is the problem" in other words, it's the difference between asking "what?" and "where?" "Can you find where THIS problem is?" "Can you find what THE problem is?"

Both are correct, but used in different situations.