I don’t know why I have only just thought of it… I do it on anki. And I assume that many people already do this on Wanikani.
When you are confused on the difference of words. Put a useful link in the “Reading Note” section. Then you can easily access the information when doing your review to reminder yourself.
For example:
育てる・育児「する」・子育て「する」
Put this in the “Reading Note”
https://up-to-you.me/article/4514
公営 vs 官営
Put this in the “Reading Note” 【公営】 と 【官営】 はどう違いますか？ | HiNative