I initially understood that kanji were always taught using the on’yomi reading and vocabulary was always taught using the kun’yomi reading, until I came across 田 and 目 and read in the FAQ [https://knowledge.wanikani.com/wanikani/japanese/onyomi-kunyomi]: “WaniKani almost always teaches the on’yomi reading with the kanji. Then you’ll learn kun’yomi readings later, with vocabulary words.”
What criteria are used to determine when kanji are sometimes taught in kun’yomi readings? Is it based on how frequently they appear in Japanese? Are the on’yomi readings used very rarely for these words? Is that why?
From my current perspective, it seems somewhat easier to me if kanji were always taught in on’yomi, but perhaps I will change my mind about this in the future.
I’m not aware that WK has published any specific fixed criteria, but the below thread includes some discussion by the team, and some speculation by others, as to why it’s sometimes done (as well as a lot of griping by people who, like you and me, would prefer that the on’yomi always be taught with the kanji).