Unfortunately with some kanji like 日 the multiple readings are all used pretty commonly (you can also look forward to learning ひ/び in the future). I don’t know if you can really intuit them so much as you just memorize the words through sheer repetition (fortunately they’re words that you would typically come across a lot). When it can, I think WK already tries to teach the most common reading with the kanji then less common readings with vocab, but there’s no perfect system around it.
The other thing is that the most basic kanji tend to have the largest variety of readings to learn so it’s a problem that’s worst in the very beginning but eventually evens out. I think it’s part of what makes kanji learning so intimidating when starting out.