as i understand it,
"rimanevano due" = "there were two remaining", [meaning some two people that remained, no further context given] or simply "two remained".
"ne rimanevano due" = "there were two of them remaining" [meaning some larger group of people, of which only two remained, the context probably comes from earlier sentences].
And you wouldn't need "ci sono" in either case, because you already have one verb (rimanevano), and another (sono) is redundant. The best English translation of "rimanevano" would be "[they] were remaining", but to understand grammar better, imagine it as "[they] remained". To say "ci sono rimanevano" is like saying "there were they remained", i.e. grammatically incorrect.
"rimanevano due" only makes sense if there was a larger group from which only two remained. both sentences could be applied to the same game of musical chairs. there is no contextual difference between the two sentences. it's just a different way to say it and maybe add a little emphasis. maybe they're telling ghost stories.
First, it's bad and unclear English. Your sentence seems to day that "it" caused "two of them" to remain. At least, that's what I, a native speaker, guess what it means. "Remain" is not used like that in English, it's intransitive (does not take an object). So "It remains" or "they remain" are good, but "it remains them" is meaningless. You would probably want to use something like "It leaves them."
On to the Italian: "rimanevano" is third person plural. So the subject here has to be "due." So it must be something like "two of them remained" or "two of them were remaining." Duo's translation "There were two of them remaining." has the same meaning, but is a less literal translation.
"There remained two of them" is perfectly fine in English, although you wouldn't hear it spoken often in this way. It is however not the imperfect tense, which is what this unit is about. For the tense to be accurate it needs to be formulated as "there were ... remaining" as the imperfect tense comes across as an action that is in progress, or incomplete in the past. Having said that, Duo seems to be pretty forgiving about this kind of thing - you just got unlucky.
You would be understood but, that would not be how an English speaker would say it. As I am learning from my studies English is backwards to many other languages. Red door, big ball, short person, two remaining. I have the problem of getting my word order right in Italian as it goes against my natural English word order. I applaud your learning Italian from English which is not your first language. Good luck with your studies! :-D