Without adding in a userscript Wanikani will only ask you to provide ONE of the readings you know as opposed to all of the readings you know. This is to save time where you will find at later levels some words have 4+ different readings and it just isnt necessary to give all of them.
The thing about multiple readings is that many Japanese texts can be read differently depending on the context. Of course wanikani will try and teach you the most ‘common’ ones though but you should make sure you are familiar with the on’yomi as these are often used in compound words for vocabulary later on (particularly with counters such as numbers, floors, people and days).
The Self-Study script might be helpful for you in between your reviews if you want to practice the readings you don’t normally use.