"What are they learning?"
I don't think so. My understanding is that you can form a question using "est-ce que" or using an inversion, not both. So you could say "Qu'apprennent-elles ?" (que = what, apprennent-elles = are they learning ?"). Or you could say "Qu'est ce qu'elles apprennent" (qu(e) = what, est-ce qu(e) = is it that?, elles apprennent = they are learning).