The two kanji I am thinking of right now are 際 and 脇
For 際, the kanji is taught as "occasion"さい and the vocab stand-alone kanji is taught as "side"きわ. I’m not saying I’m well read in Japanese, but I do read often, and not once have I seen きわ used as a stand-alone term meaning “side”, but rather, as a suffix meaning “on the brink of ~” or “about to~”, or the one Wanikani word using 土俵際. However, the stand-alone 際 one might encouter often is the さい reading, such as この際、～する際に, etc. Not only is this more common, it is one of the grammar points on the JLPT.
For 脇, the vocab meaning “armpit” is not wrong. But there is another important meaning that is used very often in literature, which is “by” or “beside”, “aside”, “to the side”, such as 道の脇に～, or ～を脇に引いた。
Just some food for thought. These are the only 2 that come to mind right now of kanji whose actual common usage differs from the (still useful) Wanikani definitions. If you can think of any more I’d love to hear them.