Forgive the confusing topic, but it seemed to fit! According to Wanikani 混じる (to get mixed in) is read まじる. But when I look up 混じる in my kanji iOS app (the app is simply called Japanese) it tells me that the reading for 混じる is こんじる.
Most confusing… is it on’yomi or kun?
Two different readings.
まじる is an intransitive godan verb. こんじる can be used transitively and intransitively and is an ichidan verb.
So in the wild, you’ll often know which reading they want with how it’s conjugated, and what transitivity the situation calls on. Dictionary form in an intransitive use-case could be more unclear.
I wonder if the こんじる reading is mostly used transitively in practice? 
I can’t really recall I’ve seen こんじる that often. 「こんじる」の用例・例文集 - 用例.jp doesn’t give any results either.
Webcorpus also shows that まじる is a lot more common.
For まじる there is also 交じる, but I get the feeling the nuance is different. In cases like this there is usually furigana above the kanji if the preferred reading in the context is different from the more widely accepted one, but since こんじる and まじる are ichidan and godan, respectively as Omun mentioned, that probably won’t be necessary as they will conjugate differently.
退ける for instance has 3 readings, but only one of them is accepted by WaniKani.
My guess is this is just phonetic drift.
Shirabe Jisho points to 混ずる
する▶️ずる
しる▶️じる
こんずる makes sense with the on’yomi reading plus する with the old rendaku style. That morphs
into こんじる and that falls out of favor for まじる.
This is all idle speculation though. 
Goo suggests that they’re the used the same:
「混じる」と同様に用いられる
I assume it’s the same as 混ざる, one of the few words where wk tells you the nuance, aka that the mixed items become indistuingishable from eachother, so paint, vs for example a salad
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