This this this! Whenever there is a rule, there is usually some kind of exception (or a bunch of them!) to be learnt alongside it 
And, as @pm215 said, WK often teaches you exceptions almost immediately after the common or standard readings, because it wants you to acquire a good sense of how that kanji might appear in the wild.
@Achilleus : Something that might be helpful is to download the userscript that tells you whether the review is asking you to give the kun or on reading (link below). I LOVE this userscript, because as well as removing any frustration or guesswork during reviews, it has also really helped my brain to distinguish kun’yomi and on’yomi over time and to better understand what functions they serve.