I know what you mean, but I read that eventually after listening to the language enough you will be able to hear differences in soft and hard sounds. I suggest finding audio clips with words like "ест" and "есть" in them and try listening to the difference. I have the same problem too just be patient and you will hear the difference subconsciously in time.
In Russian, "is eating" and "eats" are going to be expressed by just the one present tense conjugation of the verb есть. In this sentence, because it is one яблоко, it almost has to be translated as "he is eating an apple" (theoretically "he eats apple" in general in English works but it sounds funny). If it were something like Он ест мясо, then it could be translated either as "he is eating (the) meat" or "he eats meat", and you'd just have to know from further context what the person has in mind specifically.
"My brother is eating an apple" is the suggested default translation for the sentence, so either the system is glitching out (I've seen a lot of similar complaints recently from the various Russian sentences) or there was a typo in your answer.
For the second question, the single present tense conjugation of a verb in Russian covers the English idea of "does" and "is doing" (just like in German or Spanish).
My brother has an apple would be У моего брата есть яблоко. So, actually, the only word that matches is яблоко. Everything else is different.
Есть is an infinitive of the verbs "to eat", which is irregular in the present tense and has forms ем / ешь / ест/ едим/ едите/ едят. So есть can never appear in a sentence where someone "eats" or "ate" something. It can, however, appear as an infinitive attached to something (e.g., Мы хотим есть = lit. We want to eat )
The same word is also coincidentally the only surviving present form of "to be". It can an will apear in a sentence where something "exists".
Gotta admit, it throws me off that you ask for a grammatically correct English translation, because after a while the brain starts thinking in the grammar of the new language. Like, "my brother eating apple" doesn't actually make sense in English, but it is the correct meaning. Should I be penalized for thinking in Russian instead of English?