Ephraim and Manasseh were both sons of Joseph, one of the twelve brothers. So that's why there's still 12 despite the tribe of Levi not receiving any land.
Nice quiz! I think you could be a bit more lenient with type-ins though. For example, I tried "Naphthali" for "Naphtali"--I don't know necessarily if you think it should be acceptable, but I only added one letter so it'd be nice if you considered it. Similarly, you could add "Judea" as a type-in for "Judah."