"She is eating an apple."
Translation:Dia memakan apel.
Let's first look at verbs themselves. So-called words for "doing"; thus, "Aku makan/minum". Now, meN- marks the active voice. However, it is sometimes omitted for a few common verbs, such as "makan/minum".
So, in terms of difference, it depends on the context: is it spoken OR written? Informal OR formal? And so on.
Of course, this is just a working explanation. In practice, there are deviations; and some native Indonesians I have spoken to may use either form of these transitive verbs as they feel like using.