Correcting a false negative answer to a 是不是 question
There shouldn't be much chance of confusion here, because when you respond, you would be using words to indicate correctness, like 對（対）or 錯 instead of 是. So, if they respond to your question with 不是 and then you say 是 there should be no doubt that you are contradicting them, rather than affirming the correctness of their answer. Chinese is more convenient than English in this regard.

So, a few ways to answer:


不對，是蘋果
你答錯了，是蘋果
它就是蘋果
是啊


... or variations on the above.

And, of course, as the commenters mention, for the sake of pedagogy you could find out why they got the answer wrong.