This English sentence does seem like one a native speaker would be extremely unlikely to utter. A much more natural version would be "The question does not come up often."
I'm certainly of the opinion that it is strongly preferable to avoid sentences that include unnatural usages in the target language. Within the constraints of the vocab of the course to this point, I think they could have used "It is not a frequent question," which would be a good deal more natural than using "frequent" as a predicate adjective here.
The English sentences we use are really just provided by Duolingo and can be found in every language course. We cannot change them. I agree that the sentence you propose may be better, but there tends to be a reason why Duolingo structures its sentences in a certain way, with a specific content. One may assume that it follows a statistically sound formula for teaching one the language most efficiently. :)
So, even though I agree with your observation, as long as there are no serious issues with comprehending the sentence and its content, I don't see a reason to remove this sentence from the course altogether. :)