"Das Mädchen isst nicht eine Tomate."
No... not really. You would express that as "Das Mädchen isst eine Tomate nicht". "Das Mädchen isst keine Tomate" is actually correct.
"Das Mädchen isst nicht eine Tomate" is stressing that she does not even eat a single one.
Wouldn't the translation of "Das Mädchen isst nicht eine Tomate" be "The girl is not eating one tomato" e.g. she's eating more than one?
It stresses that the girl does not even eat a single tomato (see my above comment to nailtrail).
Why it can not be like this: "The girl eats not a tomato" ?!? Thank you for response.
Mainly because that's not a sentence you would say in English. While you translated every word correctly in order, it doesn't make as much sense that way. Different languages use word order differently, and I think Duolingo tries to get you to say things more correctly as opposed to close enough.