Maybe I have some type of script on because I know which one i’m being asked, but I use the script Katakana Madness to help me differentiate between on’yomi and kun’yomi readings.
If it asks for the on’yomi, you put in katakana. If it wants the kun’yomi, you put in hiragana.
Otherwise, you have to pay attention to the color codes of the questions. You will be taught all on’yomi in katakana so i’d use this only if you’re familiar with it.
I use the dark theme for wanikani so most of my colors are not set to the traditional ones, but im pretty sure vocabulary is always purple and kanji is pink.
WK will never mark you wrong if you put in the on’yomi for kun’yomi or vice versa, but it will mark you wrong if you are legitimately wrong. Guessing between the two readings for the kanji wont get you a wrong answer, but there is usually only one correct reading for vocab. You will get be marked wrong if the vocab uses a specific reading and you used a different one.
The one I can think of is 生. You learn this in Level 4.
セイ, ショウ (せい、しょう)
い, なま, う, は, き
なま and it means fresh or raw
If you have the kanji, you should insert any of the kanji readings and if would just shake if it wants a different reading.
If you have the vocab, you will get it wrong if you write “life” for the meaning and any of readings under on’yomi & kun’yomi that isnt なま .
You would have to know the vocab reading & meaning separate from the kanji. Some of the vocab will use only part of a reading from a kanji, like 作用 (action) uses only さ from 作 (さく).
This is where mnemonics become important because knowing when to use い, なま, う, は, き for any of the vocabulary that includes 生 can only be done through familiarity, memory recall/ mnemonics, and repetition.
Hope that helps!