Can WaniKani cause confusion in recognizing meaning?

So I’ve just started learning kanji, and started out with anki decks. This seemed a bit too brute force and time inefficient, since I didn’t have any anchors when trying to recognize kanjis. Since many swear by WaniKani I thought I’d try out. Now there is something that has come to my attention. When using anki (still using it for Genki vocabulary) I noticed that when I saw a kanji I didn’t immediately recognize the thing that my mind first tried to recognize was the meaning and sound connected to it. Starting out with kanji I noticed a certain friction, when it wanted me to remember “ni” (the radical but also the kanji for number 2) as “two”. However, when presented with this in my review my brain immediately goes “ni”. This happens with a couple of the other ones aswell. This might not be a problem, since so many have used WaniKani succesfully. However, I am curious as to whether any one has any thoughts (or good information), about what our brains do when we try to recognize kanji (my guess is that people have different innate techniques for it), and how to use this knowledge to ones advantage, or to avoid pitfalls.