I think the reason they don't accept that is because the word for two is standing in for the word for we. It's just a more accurate translation of the phrase, even if it's not as literal a translation as it could be. Shows the casualness of the sentence. You have to admit, there are many native English speakers that would be confused if that was given as a possible example. Not all of us know the language as well as others unfortunately.
My personal take on this: We all know that "noi" is taken to mean "we" or "us", but you never know the exact size of the group, so the "due" (which is "two" in Italian) is to indicate that there is only two people.
Then, as stated in another comment, "ci conosciamo" means "we know each other".
Basically, at least I think, the "ci" is just for added emphasis or sound (or it could be the other way around, that the "noi due" is optional, which is also said in the comments.)
Either way, the sentence now roughly says "we know each other?" so you just add "Do" in the front to make it a proper question (in English, that is.)
Here the reflexive verb "conoscersi" is used, rather than "conoscere" so it requires the reflexive pronoun - in this case "ci". Without it, it would just mean "do we know...?" http://italian.about.com/library/verb/blverb_conoscersi.htm
The Duo marking process is a fuzzy thing (as are languages), which gets updated as users suggest more exotic, albeit technically correct, answers, perhaps like yours.
This is why they let you tell them when you believe an answer should have been accepted.
You must take care in assessing the validity of your "false negative" answers though, paying attention to any grammar differences that would change the meaning of the sentence too much, whatever that might mean.
If you get marked wrong and think you shouldn't've been, check the comments, try Google Translate (though it's not perfect), and make sure you can convince yourself why your answer should be a correct one (which isn't always easy) before flagging it as a "false negative".
Remember, Duo shouldn't be your only source for learning your new language. It's the weird problems that have you scouring the Internet for answers that really get you into the learning process.
then it's wrong. Take a look at this http://web.stanford.edu/~jrb/reference/italian.html