I’m not really sure how they choose the kanji for each level. I have a feeling that neither kanji is used much outside of the transliteration of コーヒー to begin with.
However, just for your information, I don’t think the kanji form is that rare in the official names of businesses. There’s a place called Hoshino Coffee that also has a few branches outside of Japan, like in Singapore, and its name in Japanese is 星乃珈琲店. They write it that way on signage as well. I understand that it’s frustrating that the kanji were used without being taught in WK though.
I wonder what the rationale behind this is… perhaps they’re hoping that users won’t mind looking up a few words? Or perhaps there’s an assumption that users have other resources with which they’re learning Japanese (say, a dictionary like Jisho, at the least)?
Anyway, if you’re looking for another example, there’s this one from level 46 for 稲穂:
お米は私達の主食ですが、だからといって日本人全員が風に靡く美しい金色の稲穂を見た事がある訳ではありません。
Rice is our staple food, but that doesn’t mean all Japanese people have seen beautiful, golden ears of rice bowing in the breeze.
The reason I know about this one: I learnt 靡く just a few days ago (I put it on my mnemonics thread here), and I wanted to see if it was on WK. I wasn’t expecting to find it on a context sentence like that.