It’s extremely difficult to get through life in Japan without hearing 女子 (joshi), aimed at girls/young women (usually students), or 女性 (josei) for female as a gender. That’s without touching on 女 with its “jo” reading in any number of compounds. Opposite those words are 男子 (danshi) and 男性 (dansei), using their on’yomi as well, even though 男 is “otoko” as a stand-alone word and in a number of set phrases.
The goal of the kanji lessons in Wanikani, independent of the vocab lessons, is to teach you to be able to read the kanji whether you’re encountering it on its own or as a component of other words. More often than not, these compounds will utilize the on’yomi readings, which are separate from how the characters read as stand-alone vocabulary, and at any rate, you’ll need to know both for most common kanji to have anything approximating a level of literacy in Japanese. In selecting which reading to pair with the kanji as a kanji item in reviews, the site generally opts for the one which is the more useful building block for other phrases and words, which is usually but not always the on’yomi.
The goal of Wanikani is to teach you to read, and that means teaching all common readings of the kanji it includes. On a practical level, it won’t mark you incorrect for putting in the other reading during a kanji review–it’ll just shake and try to prompt you to put in the one it’s looking for, leaving the other up to vocab. That ensures you’re hitting both (or sometimes more) of the common readings for it during reviews.
(Edit – Whoops; looks like I’m just repeating statements above…)
I guess as a way of adding something new, just keep an ear out for 入 with its on’yomi reading. It’s all over the place. 入学；入社；入式；入場；入院；突入；入力（you probably have a button for this on your TV remote), and on and on.