Some syllables combined result in completely different sounds
I mean; how does e.g. ちゅう turn into 中 (spelled naka)?
Is there any rational explanation?
And it seems to me like ゅ(yu) is involved in a lot of shenanigans like that (though others are, too).
Kanji usually have more than one reading (way of being pronounced). Kanji have kun-yomi (the native Japanese reading) and on-yomi (reading taken from the Chinese pronunciation). A general rule of thumb is that kun-yomi is used when kanji appear in isolation, and on-yomi is used when you have compound words made up of two or more kanji, though there are exceptions (見方 (みかた、 point-of-view) uses the kun-yomi of both kanji, み and かた, while 本 (ほん、 book) uses the on-yomi, ほん)
Depending on the context, 中 can be read as ちゅう、じゅう、(both of which are on-yomi) or なか (kun-yomi). When alone, 中 is read as なか and means "inside/middle." In the compound word 中国 (ちゅうごく、China), 中 is read as ちゅう。
Hope this helps!
The most rational explanation I can give you is that Kanji does not bear sound but meaning. While you believe that 中 would be spelled なか, it is actually spelled differently depending on the syntactical use of it in a certain sentence.
When 中 is a noun meaning "inside" it is pronounced: なか
When 中 is a suffix, prefix meaning "middle" or "in the middle of" it is pronounced: ちゅう
I recommend Jisho.org for sentence examples and further clarifications.
As has been pointed out, kanji have different readings, like Chuu, naka, etc. The problem with the duolingo Japanese modules is that they contain some pretty bad mistakes in the pronunciation or reading of both kana and kanji. For,example は is proncounced wa when used as a participle, but often when you select it in Duolingo you hear “ha”.
Frankly the Japanese modules here are so full of errors that it’s hard to believe. I’ve seen 三日 “Mika” pronounced “San hi” when selecting words, and many other errors like this.
That’s why the Japanese is still in beta. It has a long ways to go just to be correct.