If we're asked to transcribe this from audio, and эта sounds indistinguishable and makes a correct sentence, it should probably be accepted. (German has made similar accommodations for "ist" and "isst", for example)
"It is the problem that is hard" suggests the complement: "You are not hard"; but that is not appropriate here. I think the English should be: "You are not stupid, it is that the problem is hard," or: "It's not that you are stupid, it's that the problem is hard."
They do sound pretty much the same, and since both are grammatically correct in their own way, I think Duolingo should accept both for the listening question (similar to what they do in the French course).
I agree with this. I encountered this sentence for the first time in the listening portion, and это задача трудная and эта задача трудная sound identical (both pronounced [étə] with ə being schwa). It is poor pedagogy to count эта wrong.