I think that this is just a matter of how English speakers tend to speak. It's more natural to say "The fly is on a stone", even though the sentence translates almost directly to "on the stone is a fly". The latter just sounds a bit awkward to me as a native English speaker.
No. Russian tends to place known information (topic) in the beginning of the sentence, and the new information (commentary on the topic) in the end. English usually marks known information with the, and the new information with a.
So, «На ка́мне му́ха» would mean «There’s a fly on the stone». By placing «ка́мень» in the beginning, you mark it as something the speaker knows about, the stone. And by placing му́ха in the end, you mark it as new info, something new introduced: a fly.
«Му́ха на ка́мне», on the other hand, would be translated The fly is on [a/the] stone. By placing «му́ха» in the beginning, you mark it as something known (the fly). And new information is that it’s «на ка́мне». (It can mean both a stone or the stone because even if it’s on a known stone, it would be still new information.)
Please note that the word order is not the only way to mark topic and commentary. You can use intonation for that. So, technically «му́ха на ка́мне» can mean There is a fly on the stone. if you emphasise «му́ха» with intonation: «Му́ха на камне». However, we usually don’t mark intonation in writing, so this word order is avoided in written texts.
Thank you for your long answer. That is linguistically really interesting (luckily I'm studying it). :) So, it is a strict following of the thema-rhema-process. And since the articles can't be used syntactially to mark thema and rhema the word order is used. That's really logical and interesting. Thanks =) But in the sentence "На ка́мне му́ха" the overal intonation and stress lies on "му́ха", right?
> But in the sentence "На ка́мне му́ха" the overal intonation and stress lies on "му́ха", right?
I believe usually «му́ха» would be a little emphasised, but the emphasis is much weaker than in «Му́ха на камне».
In Russian, you drop the verb to be in these cases (in others, you would have a "-" working as the verb to be). Also word order is a bit weird sometimes as it is more flexible, so you need to read the whole thing before trying to get some sense out of it.
I feel like "Есть" is used when you want to stress the fact that something exists like in "у меня есть ...". In this exercise, you are stressing the location of the fly.
It seems to me that if you are saying "There is a fly . . . " you are stressing the existence of the fly and already know the location - on the stone - as opposed to "The fly is on a stone." The location in this sentence is known, though. It's what is on it that appears to be new information. This doesn't seem to be any different than all the other sentences that say, "There is a cat in the tree" or "There is a snake at my house." All of the other ones have "есть" in the official answer. I don't see why this one wouldn't either unless it is just a matter of semantic preference.