German has no distinction between "She is eating" and "She eats". I think by using "Sie ist isst den Apfel" you are meaning that she is actually the verb eat.

in German there are no progressive tenses like "She is eating an apple" or "She was eating an apple".

Try not to use one language with the rules of another. You have to think differently in a new language. Languages are not all the same just with different words. It is like driving a totally different vehicle instead of the same one with a different paint-job.