When you use a preposition like в or на, you need to put the place in prepositional case.
Это мой стол - Nominative Яблоко на столе - Prepositional
You can read more grammar notes about this lesson on the Duolingo desktop website. They are pretty integral to helping understand the cases.
That's right, technically, although I think the definite article is implied rather than the partitive, but anyway it's not common English usage. The objective here is to teach Russian not English; I think it's better to accept only common exemplars in the English translation because if not, the English-speaking learner may think that the equivalent Russian expression is somehow non-standard.
It's common enough where I'm from. Personally, I like the idea of duolingo being extremely lenient in evaluating english translations, since the objective is learning Russian, not English. It helps my comprehension/memorization to forgo impeccable grammar and structure sentences in English to better match the Russian syntax.
I see why you may think differently though!
Desk - письменный стол http://loftinterior.ru/img/catalogue/49728107002_600.jpg
Bread can not put on the desk. Mom will be disappointed.