I think the issue is that you don’t quite understand how kanji work yet. Wanikani isn’t making it intentionally confusing–it is confusing, full stop. The vocabulary is there to help you find patterns. There are some kanji that can have 8 or more readings to memorize. None of them are “wrong”, it’s just how Japanese works.
To give some simple examples:
車 - くるま - car (kunyomi, standalone vocabulary word, refers to a car specifically).
But wanikani will teach you the しゃ reading first, because that’s the reading for the kanji when it’s a component in other words.
Ex. 1. 電車 - でんしゃ - train (lit. “Electric car”)
Ex. 2. 自転車 - じてんしゃ - bicycle (lit. " Self revolving car")
Ex. 3. 自電車 - じでんしゃ - automobile.
Another example is 海
When referring to the sea itself, it’s read as うみ. This is its standalone vocabulary word.
When learning the kanji, you will be taught the reading かい. This is the reading used when the kanji is a component in other words.
Ex. 1: 海外 - かいがい - overseas, foreign, abroad
Ex. 2. 海岸 - かいがん - coast, beach
Ex. 3. 航海 - こうかい - voyage, navigation, sailing.
You may have noticed that these are all examples of nouns. It gets more complicated than that.
Example:
下
Meaning: down, under, below, beneath
Vocabulary:
下 -した - below (noun, kunyomi reading)
下さい - ください - please give me (expression, kunyomi reading)
下げる - さげる - to lower something (verb, kunyomi reading)
下手 - へた - clumsy, unskilled, awkward (noun, na adjective, onyomi)
地下 - ちか - underground
下りる - おりる - to go down (verb, kunyomi reading)
下品 - げひん - crude, vulgar (noun, na adjective)
So, this one kanji 下 can be read as した, くだ, さ, お, げ, or か depending on the word it’s used in. Which is why wanikani teaches vocabulary to reinforce readings; most of us can’t just memorize a list of readings with no context.
I hope that helps clarify!