The vocabulary entry for 欠ける accepts “to lack” as correct answer, and I understand why, but that sounds like “to lack something”, which is incorrect. There is another word with this meaning, 欠く and the short “to lack” is more fitting here.
I think it would be better if “to lack” was moved to warning list for 欠ける and instead it accepted only the “to be lacking” answer.
I’m not sure it’s worth trying to map the vagaries of the English language on to Japanese.
If you want to say that X lacks Y, you’d use「XにはYが欠けている」* or something, 「…を欠いている」feels like newspaper Japanese.
Yeah trying to map those transitive/intransitive pairs exactly into English is just an exercise in futility. This is a topic that comes up regularly in these forums.
IMO it really doesn’t matter. If you remember that 欠ける means “to lack” then it’s good enough for the sake of WaniKani, you can work out on the nuances later when you encounter the word in meaningful context. Translating is just a crutch anyway.