For a beginner that's probably the best course of action, but as you become familiar with a language you'll find that mastering these little changes in nuance and emphasis is what makes you fluent. And even as a beginner you still have to be able to understand what's being said.
I can't exactly pinpoint it either; the "in" version is used only when speaking of people, and it seems to imply some grouping of them, e.g. "a questo gioco si gioca in due" (this game is played by two people) or "siamo in sei a tavola" (there are six of us at the table).
I'd add to f.formica's excellent answers (as always) that in English we also say "They come in hundreds"; even if not exactly equivalent the concept of IN is familiar enough.
Most importantly let's embrace and learn Italian the Italian way. Let's stick with Italian. We're being taught so that we will understand when an Italian says these sentences to us (and not argue with the natives that they say it wrong). :-).
I translated it as "we are in ninety" because I had absolutely no idea what they wanted, so I went for the literal translation, and it was marked correct. It shouldn't have been marked correct though, because that makes no sense in English. I will report it, but, wow, I'd rather lose points than have a crappy translation counted as correct.
And it's still the same 3 years later on 1 Nov 2017. I went for the completely literal meaning and it was marked correct, and i have no idea what it means - there are ninety of us, or we are in ninetieth (place), although the latter seems very unlikely to be correct - but who knows?
Siamo is "we are". As explained by f.formica above, the "in" is an idiom, and the sentence means "we are 90 (people)", or in more natural English, "there are 90 of us".
"Loro sono novanta di noi" doesn't work. That means "THEY are 90 of us", which makes no sense. However, "ci sono novanta di noi" is probably OK. Hopefully a native speaker can confirm.
that woman says siamo ina novanca. I listened to it over and over. in slo and normal speeds. She cannot pronounce. Duo loves screwing with people's heads to get an advantage. If I were speaking to her I would ask her to speak more clearly. I do well in these classes except for the audios because the people speak so badly.