I came to know from the duolingo application that Que means what. And is an interrogative sentence:
What is the question?
It translates to Spanish as
¿Cuál es la pregunta?
¿Qué es la pregunta?
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Cuál es la pregunta. You asking basically what's the question.
Qué es la pregunta? In other cases could have sense, but not here. For example: What is this? Would be: Qué es esto? ("Cuál es esto" doesn't exist)
Translated in English would be as you say "What is the question" both, with the difference that the first has sense and the second doesn't.