合う is taught in level 12. Greyed out readings are the ones that are not taught in a given kanji’s lesson. If you answer with them, the screen shakes and it asks for the one you were taught in the lesson. But most of the time they are taught somehow or another.
And technically this is just a case of okurigana getting absorbed, if you’re wondering why I mentioned 合う.
合い is the stem form of 合う, and often compounds featuring stems don’t have to include the okurigana. For instance, “entrance” can be 入り口 or 入口.
Kanjipedia, which is a digital version of the official Kanji Kentei dictionary, doesn’t list あい as a reading for 合, just あ. And the う (and any conjugations) are just inflections.
I presume WK lists あい out of courtesy, so that if you do answer with it you aren’t unfairly marked incorrect, because they don’t necessarily want to get into all of this to explain that even though it appears to have あい as a reading in something like 場合, it’s not officially a reading.