It isn't wrong, but it is a slightly different sentence.
In "Kvar kvaronoj estas unu", you are emphasizing an equality...4 * 1/4 = 1. "Kvar kvaronoj faras unu", on the other hand, emphasizes the putting together.
Now, when translating, I can't see why Duolingo shouldn't accept both. There are other sentences of this type that use "estas".