"A boy is eating a tomato."
Translation:Chłopiec je pomidora.
In most cases, you are right: in Polish, for unanimated male nouns, Accusative = Nominative, for animated male nouns, Accusative = Genitive. But, however, this is not Genitive, this is Accusative. There some nouns in Polish which have 2 acceptable forms of Accusative: colloquial, which is the same as Genitive, and strict which is the same as Nominative. And 90% of cases you will hear Genitive form, so you'd better learn this one...
To make it more complicated, there are some hundred nouns in Polish which are unanimated, but the correct form of Accusative is the same as Genitive - here is an article on that subject: Chcesz ogórka czy ogórek?
In all these phrases the default answer is "pomidora", and they were last updeted a year ago ("I eat a tomato", "The woman eats a tomato", "The boy eats a tomato"). Did you have the suggested answer with "pomidor"?
However, if you wrote "pomidor", then it should also be accepted. In writing the correct form of accusative is "pomidor", but "pomidora" is also acceptable, only it is more used in speech, see: pomidor. Many other vegetables also have 2 similar versions of accusative: burak/buraka, ogórek/ogórka, kalafior/kalafiora.